Sweep: support @tanstack/react-query version 5 #15

IvoLeist · 2023-12-08T18:32:56Z

sweep-ai · 2023-12-08T18:33:10Z

Here's the PR! #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.

convert-pheno-ui/convertPheno_client/src/code/Main.jsx

Lines 1 to 33 in 38e4eb1

	/**
	Main function for the convertPheno_client application.

	This file is part of convert-pheno-ui

	Last modified: Dec/08/2023

	Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])

	License: GPL-3.0 license
	*/

	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 { DndProvider } from "react-dnd";
	import { HTML5Backend } from "react-dnd-html5-backend";
	import App from "./App";

	const queryClient = new QueryClient();

	export default function Main() {
	return (
	<QueryClientProvider client={queryClient}>
	<DndProvider backend={HTML5Backend}>
	<ReactQueryDevtools initialIsOpen={false} />
	<HashRouter>
	<App />
	</HashRouter>
	</DndProvider>
	</QueryClientProvider>
	);

convert-pheno-ui/convertPheno_client/package.json

Lines 1 to 15 in 38e4eb1

    
           { 
        
             "name": "convert-pheno-client", 
        
             "version": "0.1.0", 
        
             "private": true, 
        
             "homepage": "./.", 
        
             "dependencies": { 
        
               "@emotion/react": "^11.11.1", 
        
               "@emotion/styled": "^11.11.0", 
        
               "@hcaptcha/react-hcaptcha": "^1.9.2", 
        
               "@mui/icons-material": "5.14.19", 
        
               "@mui/lab": "5.0.0-alpha.155", 
        
               "@mui/material": "^5.14.20", 
        
               "@mui/system": "^5.14.20", 
        
               "@mui/x-tree-view": "^6.17.0", 
        
               "@tanstack/react-query": "4.36.1",

convert-pheno-ui/convertPheno_client/package.json

Lines 15 to 30 in 38e4eb1

    
           "@tanstack/react-query": "4.36.1", 
        
           "ag-grid-community": "^31.0.0", 
        
           "ag-grid-react": "^31.0.0", 
        
           "axios": "^1.6.2", 
        
           "babel-plugin-istanbul": "^6.1.1", 
        
           "filepond": "^4.30.4", 
        
           "filepond-plugin-file-validate-size": "^2.2.8", 
        
           "filepond-plugin-file-validate-type": "^1.2.8", 
        
           "keycloak-js": "^23.0.1", 
        
           "react": "^18.2.0", 
        
           "react-bootstrap": "^2.9.1", 
        
           "react-dnd": "^16.0.1", 
        
           "react-dnd-html5-backend": "^16.0.1", 
        
           "react-dom": "^18.2.0", 
        
           "react-error-boundary": "^4.0.11", 
        
           "react-filepond": "^7.1.2",

convert-pheno-ui/convertPheno_client/package.json

Lines 120 to 135 in 38e4eb1

    
             "not ie <= 11", 
        
             "not op_mini all" 
        
           ], 
        
           "devDependencies": { 
        
             "@cypress/code-coverage": "^3.10.4", 
        
             "@cypress/react18": "^2.0.0", 
        
             "@istanbuljs/nyc-config-typescript": "^1.0.2", 
        
             "@modyfi/vite-plugin-yaml": "^1.0.4", 
        
             "@storybook/addon-actions": "^7.0.5", 
        
             "@storybook/addon-essentials": "^7.0.5", 
        
             "@storybook/addon-links": "^7.0.5", 
        
             "@storybook/cli": "^7.0.5", 
        
             "@storybook/react": "^7.0.5", 
        
             "@storybook/react-webpack5": "^7.0.5", 
        
             "@tanstack/react-query-devtools": "^5.13.3", 
        
             "@testing-library/cypress": "^8.0.2",

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

convert-pheno-ui/convertPheno_client/src/code/views/conversion/hooks/finishedJobs.jsx

Lines 1 to 38 in 38e4eb1

	/**
	helper function query finished jobs

	This file is part of convert-pheno-ui

	Last modified: Dec/08/2023

	Copyright (C) 2022-2023 Ivo Christopher Leist - CNAG ([email protected])

	License: GPL-3.0 license
	*/

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

	export default function useFinishedJobs(props) {
	const { query, conversionFinished } = props;
	const { jobId } = query;

	return useQuery(
	["finishedJob", jobId],
	async () => {
	const res = await apiRequest(
	"jobs/job",
	JSON.stringify(query)
	);
	return res.data;
	},
	{
	enabled: query.jobId !== undefined && !conversionFinished,
	// maybe do a retry depending on the error -> no when the job is not found
	retry: 0,
	retryDelay: 10,
	cacheTime: 200,
	staleTime: 300_000,
	onSuccess: (data) => {},
	}
	);

Step 2: ⌨️ Coding

Modify convertPheno_client/package.json ✓ f513bcc 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",

Running GitHub Actions for convertPheno_client/package.json ✓ Edit

Check convertPheno_client/package.json with contents:
Ran GitHub Actions for f513bccd85841122702bec520378e423645c1754:

Modify convertPheno_client/src/code/Main.jsx ✓ c2148dd 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 (

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:

Modify convertPheno_client/src/code/views/conversion/ components/clinicalData/ClinicalData.jsx ✓ bd4f8f8 [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({

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:

Modify convertPheno_client/src/code/views/conversion/ components/submission/Submission.jsx ✓ cd2e1c9 [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({

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:

Modify convertPheno_client/src/code/views/conversion/hooks/finishedJobs.jsx ✓ 0cb2675 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
}
);
}

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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IvoLeist added the sweep Assigns Sweep to an issue or pull request. label Dec 8, 2023

github-actions bot assigned IvoLeist Dec 8, 2023

sweep-ai bot linked a pull request Dec 8, 2023 that will close this issue

Upgrade @tanstack/react-query to version 5 (✓ Sandbox Passed) #16

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Sweep: support @tanstack/react-query version 5 #15

Sweep: support @tanstack/react-query version 5 #15

IvoLeist commented Dec 8, 2023 •

edited by sweep-ai bot

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sweep-ai bot commented Dec 8, 2023 •

edited

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Sweep: support @tanstack/react-query version 5 #15

Sweep: support @tanstack/react-query version 5 #15

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IvoLeist commented Dec 8, 2023 • edited by sweep-ai bot Loading

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sweep-ai bot commented Dec 8, 2023 • edited Loading

Here's the PR! #16. See Sweep's process at dashboard.

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Sandbox Execution ✓

Step 1: 🔎 Searching

Step 2: ⌨️ Coding

Step 3: 🔁 Code Review

🎉 Latest improvements to Sweep:

IvoLeist commented Dec 8, 2023 •

edited by sweep-ai bot

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sweep-ai bot commented Dec 8, 2023 •

edited

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