Sweep: support @tanstack/react-query version 5

Here's the PR! https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/pull/16. See Sweep's process at dashboard.

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Sandbox Execution ✓

Here are the sandbox execution logs prior to making any changes:

Sandbox logs for 38e4eb1

Checking convertPheno_client/package.json for syntax errors... ✅ convertPheno_client/package.json has no syntax errors! 1/1 ✓
Checking convertPheno_client/package.json for syntax errors...
✅ convertPheno_client/package.json has no syntax errors!

Sandbox passed on the latest main, so sandbox checks will be enabled for this issue.

Step 1: 🔎 Searching

I found the following snippets in your repository. I will now analyze these snippets and come up with a plan.

Some code snippets I think are relevant in decreasing order of relevance (click to expand). If some file is missing from here, you can mention the path in the ticket description.

https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/blob/38e4eb1b0a33f66378921537dd9fef1be6d42348/convertPheno_client/src/code/Main.jsx#L1-L33 https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/blob/38e4eb1b0a33f66378921537dd9fef1be6d42348/convertPheno_client/package.json#L1-L15 https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/blob/38e4eb1b0a33f66378921537dd9fef1be6d42348/convertPheno_client/package.json#L15-L30 https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/blob/38e4eb1b0a33f66378921537dd9fef1be6d42348/convertPheno_client/package.json#L120-L135 https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/blob/38e4eb1b0a33f66378921537dd9fef1be6d42348/convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx#L1-L21 https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/blob/38e4eb1b0a33f66378921537dd9fef1be6d42348/convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx#L1-L22 https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/blob/38e4eb1b0a33f66378921537dd9fef1be6d42348/convertPheno_client/src/code/views/conversion/hooks/finishedJobs.jsx#L1-L38

Step 2: ⌨️ Coding

[X] Modify convertPheno_client/package.json ✓ https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/commit/f513bccd85841122702bec520378e423645c1754 Edit
Modify convertPheno_client/package.json with contents:
• Change the version of @tanstack/react-query in the "dependencies" section from "4.36.1" to "5.x.x", where "x.x" is the latest minor and patch version of @tanstack/react-query version 5.

+++ @@ -12,7 +12,7 @@ "@mui/material": "^5.14.20", "@mui/system": "^5.14.20", "@mui/x-tree-view": "^6.17.0",

"@tanstack/react-query": "4.36.1",
"@tanstack/react-query": "5.x.x", "ag-grid-community": "^31.0.0", "ag-grid-react": "^31.0.0", "axios": "^1.6.2",

[X] Running GitHub Actions for convertPheno_client/package.json ✓ Edit
Check convertPheno_client/package.json with contents:

Ran GitHub Actions for f513bccd85841122702bec520378e423645c1754:

[X] Modify convertPheno_client/src/code/Main.jsx ✓ https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/commit/c2148dd99c643bfa64459774b66b10253ee54d50 Edit
Modify convertPheno_client/src/code/Main.jsx with contents:
• Replace the deprecated methods from @tanstack/react-query with their new equivalents in version 5. The exact changes will depend on which methods are deprecated in the new version.

+++ @@ -12,13 +12,13 @@

import React from "react"; import { HashRouter } from "react-router-dom"; -import { QueryClient, QueryClientProvider } from "@tanstack/react-query"; -import { ReactQueryDevtools } from "@tanstack/react-query-devtools"; +import { createQueryClient, QueryClientProvider } from "@tanstack/react-query"; +import { ReactQueryDevtools } from "@tanstack/react-query/devtools"; import { DndProvider } from "react-dnd"; import { HTML5Backend } from "react-dnd-html5-backend"; import App from "./App";

-const queryClient = new QueryClient(); +const queryClient = createQueryClient();

export default function Main() { return (

[X] Running GitHub Actions for convertPheno_client/src/code/Main.jsx ✓ Edit
Check convertPheno_client/src/code/Main.jsx with contents:

Ran GitHub Actions for c2148dd99c643bfa64459774b66b10253ee54d50:

[X] Modify convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx ✓ https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/commit/bd4f8f8d775d957bdf98aa921a8a3cf65a89137b [Edit](https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/edit/sweep/upgrade-react-query/convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx)
Modify convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx with contents:
• Replace the deprecated methods from @tanstack/react-query with their new equivalents in version 5. The exact changes will depend on which methods are deprecated in the new version.

+++ @@ -12,7 +12,7 @@

import React, { useEffect, useState } from "react"; import { useLocation } from "react-router-dom"; -import { useQueryClient } from "@tanstack/react-query"; +import { useQueryClient, QueryClient } from "@tanstack/react-query";

import SimpleTabs from "./components/simpleTabs/SimpleTabs"; import useQueryBuilder from "./components/queryBuilder/hooks/useQueryBuilder"; @@ -28,7 +28,7 @@ */ const { outputFormats, jobId } = props; const location = useLocation();

const queryClient = useQueryClient();
const queryClient = new QueryClient();

const [tabValue, setTabValue] = useState(0); const [shownColumns, setShownColumns] = useState({}); @@ -59,7 +59,7 @@ });

useEffect(() => {
queryClient.invalidateQueries("resultsQuery", { refetchActive: true });
queryClient.invalidateQueries("resultsQuery"); }, [location, queryClient, shownColumns]);

const renderQueryBuilder = useQueryBuilder({

[X] Running GitHub Actions for convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx ✓ [Edit](https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/edit/sweep/upgrade-react-query/convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx)
Check convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx with contents:

Ran GitHub Actions for bd4f8f8d775d957bdf98aa921a8a3cf65a89137b:

[X] Modify convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx ✓ https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/commit/cd2e1c955175daaaf6824c858c03917e1e8fd06a [Edit](https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/edit/sweep/upgrade-react-query/convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx)
Modify convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx with contents:
• Replace the deprecated methods from @tanstack/react-query with their new equivalents in version 5. The exact changes will depend on which methods are deprecated in the new version.

+++ @@ -38,7 +38,7 @@ const [error, setError] = useState(false); const [retryTime, setRetryTime] = useState(10);

const queryClient = useQueryClient();
const queryClient = new QueryClient(); const navigate = useNavigate();

const { status, data } = useFileConversions({

[X] Running GitHub Actions for convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx ✓ [Edit](https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/edit/sweep/upgrade-react-query/convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx)
Check convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx with contents:

Ran GitHub Actions for cd2e1c955175daaaf6824c858c03917e1e8fd06a:

[X] Modify convertPheno_client/src/code/views/conversion/hooks/finishedJobs.jsx ✓ https://github.com/CNAG-Biomedical-Informatics/convert-pheno-ui/commit/0cb26750b4b258dce1e0f2cb081e7c14ef089c23 Edit
Modify convertPheno_client/src/code/views/conversion/hooks/finishedJobs.jsx with contents:
• Replace the deprecated methods from @tanstack/react-query with their new equivalents in version 5. The exact changes will depend on which methods are deprecated in the new version.

+++ @@ -10,7 +10,7 @@ License: GPL-3.0 license */

-import { useQuery } from "@tanstack/react-query"; +import { useQuery } from "react-query"; import apiRequest from "../../../ApiRequest";

export default function useFinishedJobs(props) { @@ -34,6 +34,8 @@ cacheTime: 200, staleTime: 300_000, onSuccess: (data) => {},

refetchOnWindowFocus: false,
refetchOnReconnect: false } ); }

[X] Running GitHub Actions for convertPheno_client/src/code/views/conversion/hooks/finishedJobs.jsx ✓ Edit
Check convertPheno_client/src/code/views/conversion/hooks/finishedJobs.jsx with contents:

Ran GitHub Actions for 0cb26750b4b258dce1e0f2cb081e7c14ef089c23:

Step 3: 🔁 Code Review

I have finished reviewing the code for completeness. I did not find errors for sweep/upgrade-react-query.

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CNAG-Biomedical-Informatics / convert-pheno-ui