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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,125 @@ | ||
| import React, { useState } from 'react'; | ||
| import { QueryClient, QueryClientProvider } from 'react-query'; | ||
| import { rest } from 'msw'; | ||
| import GWASWorkflowList from './GWASWorkflowList'; | ||
| import { gwasStatus } from '../GWASWizard/shared/constants'; | ||
|
|
||
| export default { | ||
| title: 'Tests2/GWASUI/WorkflowList', | ||
| component: GWASWorkflowList, | ||
| }; | ||
|
|
||
| const mockedQueryClient = new QueryClient({ | ||
| defaultOptions: { | ||
| queries: { retry: false }, | ||
| }, | ||
| }); | ||
|
|
||
| const MockTemplate = () => { | ||
|
|
||
| return ( | ||
| <QueryClientProvider client={mockedQueryClient}> | ||
| <GWASWorkflowList refetchInterval={1000} /> | ||
| </QueryClientProvider> | ||
| ); | ||
| }; | ||
|
|
||
| let requestCount = 0; | ||
| let rowCount = 1; | ||
| const getMockPhase = (requestCount) => { | ||
| if (requestCount % 2 == 0) { | ||
| return gwasStatus.running; | ||
| } else if (requestCount % 5 == 0) { | ||
| return gwasStatus.failed; | ||
| } else { | ||
| return gwasStatus.succeeded; | ||
| } | ||
| } | ||
|
|
||
| let workflowList = []; | ||
|
|
||
| const getMockWorkflowList = () => { | ||
| requestCount++; | ||
| // simulate a new workflow only at each 3rd request: | ||
| if (requestCount % 3 == 0) { | ||
| workflowList.splice(0, 0, {"name" : "argo-wrapper-workflow-" + requestCount, "phase": getMockPhase(requestCount)}); | ||
| rowCount++; | ||
| } | ||
| // simulate status change of some recent items at each 10th request: | ||
| if (rowCount % 5 == 0) { | ||
| // just some status that is not used in getMockPhase: | ||
| workflowList[2].phase = gwasStatus.pending; | ||
| workflowList[3].phase = gwasStatus.pending; | ||
| } | ||
| return workflowList; | ||
| } | ||
|
|
||
| export const MockedSuccess = MockTemplate.bind({}); | ||
| MockedSuccess.parameters = { | ||
| msw: { | ||
| handlers: [ | ||
| rest.get('http://:argowrapperpath/ga4gh/wes/v2/workflows', (req, res, ctx) => { | ||
| const { argowrapperpath } = req.params; | ||
| console.log(argowrapperpath); | ||
| return res( | ||
| ctx.delay(200), | ||
| ctx.json(getMockWorkflowList()), | ||
| ); | ||
| }), | ||
| rest.get('http://:argowrapperpath/ga4gh/wes/v2/status/:workflowid', (req, res, ctx) => { | ||
| const { argowrapperpath } = req.params; | ||
| const { workflowid } = req.params; | ||
| console.log(argowrapperpath); | ||
| console.log(workflowid); | ||
|
|
||
| return res( | ||
| ctx.delay(500), | ||
| ctx.json({"name": workflowid, | ||
| "wf_name": workflowid + " name", | ||
| "arguments":{"parameters":[ | ||
| {"name":"source_id","value":"2"}, | ||
| {"name":"case_cohort_definition_id","value":"300"}, | ||
| {"name":"control_cohort_definition_id","default":"-1","value":"-1"}, | ||
| {"name":"n_pcs","value":"3"}, | ||
| {"name":"covariates","value":"ID_2000006885 ID_2000000708"}, | ||
| {"name":"outcome","value":"ID_2000006886"}, | ||
| {"name":"out_prefix","default":"genesis_vadc","value":"123456789"}, | ||
| {"name":"maf_threshold","value":"0.01"},{"name":"imputation_score_cutoff","value":"0.3"}, | ||
| {"name":"hare_population","value":"Hispanic"}, | ||
| {"name":"prefixed_hare_concept_id","default":"ID_2000007027","value":"ID_2000007027"}, | ||
| {"name":"internal_api_env","default":"default","value":"qa-mickey"}, | ||
| {"name":"genome_build","default":"hg19","value":"hg19","enum":["hg38","hg19"]}, | ||
| {"name":"pca_file","value":"/commons-data/pcs.RData"}, | ||
| {"name":"relatedness_matrix_file","value":"/commons-data/abc.RData"}, | ||
| {"name":"n_segments","value":"0"}, | ||
| {"name":"segment_length","default":"2000","value":"2000"}, | ||
| {"name":"variant_block_size","default":"1024","value":"100"}, | ||
| {"name":"mac_threshold","value":"0"}, | ||
| {"name":"gds_files","value":"[\"/commons-data/gds/chr1.merged.vcf.gz.gds\", \"/commons-data/gds/chr2.merged.vcf.gz.gds\"]"}]}, | ||
| "phase": getMockPhase(requestCount), | ||
| "progress":"6/6", | ||
| "startedAt":"2022-07-01T17:29:29Z", | ||
| "finishedAt":"2022-07-01T17:33:13Z", | ||
| "outputs":{"parameters":[{"name":"gwas_archive_index", | ||
| "value": | ||
| "{\n \"baseid\": \"123456-789-1023-1234-d123545e\",\n \"did\": \"123456-654-123-123-f654987123\",\n \"rev\": \"123456c789\"\n}"} | ||
| ] | ||
| } | ||
| }), | ||
| ); | ||
| }), | ||
| ], | ||
| }, | ||
| }; | ||
|
|
||
| export const MockedError = MockTemplate.bind({}); | ||
| MockedError.parameters = { | ||
| msw: { | ||
| handlers: [ | ||
| rest.post('', (req, res, ctx) => res( | ||
| ctx.delay(800), | ||
| ctx.status(403), | ||
| )), | ||
| ], | ||
| }, | ||
| }; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,116 @@ | ||
| import React, { useState } from "react"; | ||
| import { Space, Button, Popconfirm } from "antd"; | ||
| import SelectStudyPopulation from "./SelectStudyPopulation/SelectStudyPopulation"; | ||
| import "./GWASV2.css"; | ||
|
|
||
| const GWASContainer = () => { | ||
| const [current, setCurrent] = useState(0); | ||
| const [ | ||
| selectedStudyPopulationCohort, | ||
| setSelectedStudyPopulationCohort, | ||
| ] = useState({}); | ||
| const gwasSteps = [ | ||
| { | ||
| title: "Step 1", | ||
| description: "Select Study Population", | ||
| }, | ||
| { | ||
| title: "Step 2", | ||
| description: "Select Outcome Phenotypes", | ||
| }, | ||
| { | ||
| title: "Step 3", | ||
| description: "Select Covariate Phenotype", | ||
| }, | ||
| { | ||
| title: "Step 4", | ||
| description: "Configure GWAS", | ||
| }, | ||
| ]; | ||
|
|
||
| const generateStep = () => { | ||
| // steps 2 & 3 very similar | ||
| switch (current) { | ||
| case 0: | ||
| // select study population | ||
| return ( | ||
| <SelectStudyPopulation | ||
| selectedStudyPopulationCohort={selectedStudyPopulationCohort} | ||
| setSelectedStudyPopulationCohort={setSelectedStudyPopulationCohort} | ||
| current={current} | ||
| /> | ||
| ); | ||
| case 1: | ||
| // outcome (customdichotomous or not) | ||
| return <React.Fragment>step 2</React.Fragment>; | ||
| case 2: | ||
| // covariates (customdichtomous or not) | ||
| return <React.Fragment>step 3</React.Fragment>; | ||
| case 3: | ||
| // all other input (mafs, imputation, etc), review, and submit | ||
| return <React.Fragment>step 4</React.Fragment>; | ||
| default: | ||
| // required for eslint | ||
| return null; | ||
| } | ||
| }; | ||
| return ( | ||
| <React.Fragment> | ||
| {/* Inline style block needed so centering rule doesn't impact other workflows */} | ||
| <style>{`.analysis-app__actions > div:nth-child(1) {margin: 0 auto; }`}</style> | ||
| <div className="GWASV2"> | ||
| <Space direction={"vertical"} style={{ width: "100%" }}> | ||
| <div className="steps-content"> | ||
| <Space | ||
| direction={"vertical"} | ||
| align={"center"} | ||
| style={{ width: "100%" }} | ||
| > | ||
| {generateStep(current)} | ||
| </Space> | ||
| </div> | ||
| <div className="steps-action"> | ||
| <Button | ||
| className="GWASUI-navBtn GWASUI-navBtn__next" | ||
| type="primary" | ||
| onClick={() => { | ||
| setCurrent(current - 1); | ||
| }} | ||
| disabled={current < 1 ? true : false} | ||
| > | ||
| Previous | ||
| </Button> | ||
| <Popconfirm | ||
| title="Are you sure you want to leave this page?" | ||
| // onConfirm={() => resetGWASType()} | ||
| okText="Yes" | ||
| cancelText="No" | ||
| > | ||
| <Button type="link" size="medium"> | ||
| Select Different GWAS Type | ||
| </Button> | ||
| </Popconfirm> | ||
| {current < gwasSteps.length - 1 && ( | ||
| <Button | ||
| data-tour="next-button" | ||
| className="GWASUI-navBtn GWASUI-navBtn__next" | ||
| type="primary" | ||
| onClick={() => { | ||
| setCurrent(current + 1); | ||
| }} | ||
| // disabled={!nextButtonEnabled} | ||
| > | ||
| Next | ||
| </Button> | ||
| )} | ||
| {current === gwasSteps.length - 1 && ( | ||
| <div className="GWASUI-navBtn" /> | ||
| )} | ||
| </div> | ||
| </Space> | ||
| </div> | ||
| </React.Fragment> | ||
| ); | ||
| }; | ||
|
|
||
| export default GWASContainer; |
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