From b84bfe0711f11e5da123da3330b2aafe2cc1bcae Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sun, 5 May 2024 17:59:29 +0530 Subject: [PATCH 1/3] fix --- src/components/TaskCreate.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/components/TaskCreate.js b/src/components/TaskCreate.js index 237eb47..c9a48c7 100644 --- a/src/components/TaskCreate.js +++ b/src/components/TaskCreate.js @@ -14,7 +14,7 @@ const TaskCreateRuns = ({ isLoggedIn, showToast }) => { return (
; + />
); }; From ef68389a14fa7fc307774d1c1f211a074639934f Mon Sep 17 00:00:00 2001 From: Javed Habib Date: Sun, 5 May 2024 18:08:08 +0530 Subject: [PATCH 2/3] wes --- cypress/videos/spec.cy.js.mp4 | Bin 14178 -> 16928 bytes src/components/ManageWorkflows.js | 179 +------ src/components/RunWorkflow.js | 797 +----------------------------- 3 files changed, 8 insertions(+), 968 deletions(-) diff --git a/cypress/videos/spec.cy.js.mp4 b/cypress/videos/spec.cy.js.mp4 index b430ba730a67899328528a6dd9e125937beadf70..62518be8657864fe439380bdd4d28baca7e52938 100644 GIT binary patch delta 13101 zcmZ{K1yohf*Y>$wx=R|RyBq25?gkM_=?1xkba$r+2-4l5lypc55-Qz_fFQgF{gwZ3 zeXO-PF}r5ZJ~Q*|xf_lJ&mjp+Z~{8DEb{Phn77GmP%;b&005{Z^1@_rSlDlqEuh57 z6!6H&J@CrE87Pw35S&nGC9;lrihKVM$;Xtr_pb<2@*#pOJgr1FPqGU_MBGvApaNYX|gOq}E2vP=KSf}KHv%fI|Bc=eAUJTh*qRYWjAc$@qPQ53crA;?yp zd@8#h58sZv!{BKgDGU?r$VQf6Q7gg3M%_KM{>jp?hUz?ScATZ~PV_y+i(pjqZ%+%R zH>sEx2A9dhTDsJT>^!qbc?(r{ZM}UJgbd(HaB=Vmd^@FC?E&VXG=NCryMz%&tDMb* 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zHFwm>`|?{}BzRfQBF(z3-8xmxi=?{dUM1K!C*jYYYF!_!HFqQ?mhB_Z z`?=0$9gg>!lS#JK2K@KCzPJ&BaAbfCg>5JR>2kIwoh!w~iPdF_T&{HtA+932wKPE) z8Zn?LHmKmB+^FL)pLV4@x`Y3|u_tcIGXLW+m2$!6=Z<*7%l5pvOdNr{OV?ZDdNaC_ z|GU1SV?iLWJUDm$uY|9F$o~P)W*WwiK6`mP$1qEqOd|6&$1S2)hALolkX&m=m{+|v zI*YYaCyKx|UL3ocu%a`A0OvRD?mdQr^Xb=Jd;_mFB(Fv&@4k^xVbeR|9s$nA^ez z^sTGAG0F~7v}MrV40Ia*_ss}~FnWpc{G?#F#2S7sC>WT;9exog= { const navigate = useNavigate(); - const [workflows, setWorkflows] = React.useState(null); - const [query, setQuery] = React.useState(''); - // const [nextToken, setNextToken] = React.useState(null); - // const [loading, setLoading] = React.useState(false); - // var token = localStorage.getItem("params"); - // token = JSON.parse(token); - // token = token ? token.access_token : null; useEffect(() => { if (isLoggedIn === 'false') { @@ -19,174 +11,9 @@ const ManageWorkflows = ({ isLoggedIn, showToast }) => { } }, [isLoggedIn]); - useEffect(() => { - (async function fetchWorkflows() { - try { - const res = await axios.get(`${host_uri_wes}/runs`); - setWorkflows(res.data); - // setNextToken(res.data.next_page_token); - } catch (e) { - console.log(e); - showToast('error', 'Server error!'); - } - // setInterval(handleRefresh, 5000); - })(); - }, []); - - // const handleRefresh = async () => { - // if (workflows === null) return; - // try { - // const res = await axios.get(`${host_uri_wes}/runs`, { - // headers: { - // Authorization: `Bearer ${token}`, - // }, - // }); - // let tempWorkflows = workflows; - // console.log(workflows, tempWorkflows, res.data); - // // if (tempWorkflows[0].run_id !== res.data.runs[0].run_id) { - // // tempWorkflows.unshift(res.data.runs[0]); - // // } - // // setWorkflows(tempWorkflows); - // } catch (e) { - // showToast("error", "Server error!"); - // } - // }; - - // const loadMore = async () => { - // setLoading(true); - // try { - // const res = await axios.get(`${host_uri_wes}/runs?${nextToken !== "" ? "page_token=" + nextToken : ""}`, { - // headers: { - // Authorization: `Bearer ${token}`, - // }, - // }); - // setWorkflows([...workflows, ...res.data.runs]); - // setNextToken(res.data.next_page_token); - // } catch (error) { - // showToast("error", "Server error!"); - // } - // setLoading(false); - // }; - // console.log(workflows); - - // const fetchWorkflow = async (id) => { - // try { - // const res = await axios.get(`${host_uri_wes}/runs/${id}`, { - // headers: { - // Authorization: `Bearer ${token}`, - // }, - // }); - // let tempworkflows = workflows; - // let index = tempworkflows.findIndex((workflow) => workflow.id === id); - // tempworkflows[index]. = - // return res.data; - // } catch (error) { - // showToast("error", "Server error!"); - // } - // }; - - const renderRuns = () => { - console.log(workflows); - if (workflows === null || workflows === undefined) { - return
; - } else if (workflows.length === 0) { - return
; - } else { - return ( - - {workflows.map((workflow, i) => - query === '' || workflow.run_id.includes(query) ? ( - navigate(`/manage/${workflow.run_id}`)} - > - - {i + 1} - - - {workflow.run_id} - - - {workflow.run_status} - - - ) : ( - <> - ) - )} - - ); - } - }; - return ( -
-
- setQuery(e.target.value)} - > -
- - - - - - - - - {renderRuns()} -
- # - - Run ID - - Run Status -
-
- {workflows === null ? ( -
- - - - -
- ) : workflows.length === 0 ? ( -

- No workflows found -

- ) : ( -
- )} -
+
+
); }; diff --git a/src/components/RunWorkflow.js b/src/components/RunWorkflow.js index 069553f..2087534 100644 --- a/src/components/RunWorkflow.js +++ b/src/components/RunWorkflow.js @@ -1,37 +1,8 @@ -import React, { useEffect, useState } from 'react'; -// import validator from "validator"; -import yaml from 'js-yaml'; +import React, { useEffect} from 'react'; import { useNavigate } from 'react-router-dom'; -import axios from 'axios'; -import CodeEditor from '@uiw/react-textarea-code-editor'; -import Files from 'react-files'; -import Marquee from 'react-fast-marquee'; -import { host_uri_wes } from '../config'; -import { confirmAlert } from 'react-confirm-alert'; -import { Document, Page, pdfjs } from 'react-pdf'; -import 'react-pdf/dist/Page/AnnotationLayer.css'; -import 'react-pdf/dist/Page/TextLayer.css'; +import ECCClientGa4ghWesCreateRun from '@elixir-cloud/wes/dist/react/create-run'; const RunWorkflow = ({ isLoggedIn, showToast }) => { - // Pdfjs worker - pdfjs.GlobalWorkerOptions.workerSrc = `//cdnjs.cloudflare.com/ajax/libs/pdf.js/${pdfjs.version}/pdf.worker.js`; - - const [workflow_type, set_workflow_type] = useState('CWL'); - const [workflow_version, set_workflow_version] = useState('v1.0'); - const [workflow_url, set_workflow_url] = useState(''); - const [workflow_url_error, set_workflow_url_error] = useState(''); - const [workflow_params, set_workflow_params] = useState(''); - const [workflow_params_error, set_workflow_params_error] = useState(''); - const [workflow_attachments, set_workflow_attachments] = useState([]); - const [workflow_attachments_error, set_workflow_attachments_error] = - useState(''); - const [showAdvance, setShowAdvance] = useState(false); - const [workflow_engine_params, set_workflow_engine_params] = useState(''); - const [workflow_engine_params_error, set_workflow_engine_params_error] = - useState(''); - const [tags, setTags] = useState([]); - const [tags_error, set_tags_error] = useState([]); - const [loading, setLoading] = useState(false); const navigate = useNavigate(); useEffect(() => { @@ -40,768 +11,10 @@ const RunWorkflow = ({ isLoggedIn, showToast }) => { } }, [isLoggedIn]); - const handleTypeChange = (e) => { - set_workflow_type(e.target.value); - if (e.target.value === 'CWL') { - set_workflow_version('v1.0'); - } else if (e.target.value === 'SMK') { - set_workflow_version('6.10.0'); - } else { - set_workflow_version('DSL1'); - } - }; - - const renderTags = () => { - return ( - <> - {tags.map((tag, i) => { - return ( - <> -
- handleChangeTag(true, i, e)} - className="bg-gray-100 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block w-full p-2.5 mr-3" - placeholder="Please enter a key." - /> - handleChangeTag(false, i, e)} - className="bg-gray-100 text-gray-900 text-sm rounded-lg focus:ring-blue-500 focus:border-blue-500 block w-full p-2.5" - placeholder="Please enter a value." - /> - handleRemoveTag(i)} - > - - - - -
- {tags_error[i] !== '' ? ( -
{tags_error[i]}
- ) : ( - <> - )} - - ); - })} - - ); - }; - - const handleChangeTag = (isKey, i, e) => { - let tempTags = tags; - if (isKey) { - tempTags[i].key = e.target.value; - } else { - tempTags[i].value = e.target.value; - } - tempTags = [...tempTags]; - setTags(tempTags); - }; - - const handleAddTag = () => { - let tempTags = tags; - tempTags = [...tempTags, { key: '', value: '' }]; - setTags(tempTags); - set_tags_error([...tags_error, '']); - }; - - const handleRemoveTag = (i) => { - let tempTags = tags; - tempTags.splice(i, 1); - tempTags = [...tempTags]; - setTags(tempTags); - tempTags = tags_error; - tempTags.splice(i, 1); - tempTags = [...tempTags]; - set_tags_error(tempTags); - }; - - const handleAttachmentChange = (e) => { - const tempAttachment = [...workflow_attachments, ...e]; - set_workflow_attachments(tempAttachment); - }; - // const handleSubmit = async (e) => { - // e.preventDefault(); - // const formData = new FormData(); - // formData.append("workflow_url", "https://github.com/ga4gh/workflow-execution-service-schemas/blob/c3b19854240c4fcbaf3483e22b19db0a918a7ee5/openapi/paths/runs.yaml#L89"); - // formData.append("workflow_params", `{"text":"hello world"}`); - // formData.append("workflow_type_version", "<=6.10.0"); - // formData.append("workflow_type", "SMK"); - // const res = await axios.post("https://wes.rahtiapp.fi/ga4gh/wes/v1/runs", formData, { - // headers: { - // "content-type": "multipart/form-data", - // Accept: "application/json", - // "Access-Control-Allow-Origin": "*", - // "Access-Control-Allow-Headers": "*", - // }, - // }); - // console.log(res); - // }; - - const handleSubmit = async (e) => { - e.preventDefault(); - set_workflow_url_error(''); - set_workflow_params_error(''); - set_workflow_engine_params_error(''); - set_workflow_attachments_error(''); - - const formData = new FormData(); - // console.log(workflow_type); - formData.append('workflow_type', workflow_type); - // console.log(workflow_version); - if (workflow_type === 'NFL') { - formData.append('workflow_type_version', '21.04.0'); - } else { - formData.append('workflow_type_version', workflow_version); - } - - // workflow_url - if (workflow_url === '') { - set_workflow_url_error('Workflow URL is required!'); - return; - } - // else if (!validator.isURL(workflow_url)) { - // set_workflow_url_error("Workflow URL is not a valid URL!"); - // return; - // } - // console.log(workflow_url); - formData.append('workflow_url', workflow_url); - // workflow_url end - - // workflow_params - if (workflow_params === '') { - set_workflow_params_error('Workflow parameters is required!'); - return; - } - let workflow_params_json = ''; - try { - // console.log(workflow_params); - workflow_params_json = await yaml.load(workflow_params); - // console.log(workflow_params_json); - } catch (e) { - set_workflow_params_error('Workflow parameters is not a valid YAML!'); - return; - } - workflow_params_json = JSON.stringify(workflow_params_json); - // console.log(workflow_params_json); - formData.append('workflow_params', workflow_params_json); - // workflow_params end - - // workflow_attachment - if (workflow_attachments.length > 20) { - set_workflow_attachments_error( - 'Workflow attachments must be less that 20.' - ); - return; - } - for (const item of workflow_attachments) { - if (item.size / 1000 > 500) { - set_workflow_attachments_error( - 'Workflow attachments must be less that 500 KB.' - ); - return; - } else { - // console.log(item); - formData.append(`workflow_attachment`, item); - } - } - // workflow_attachment end - - // workflow_engine_params - let workflow_engine_params_json = ''; - if (workflow_engine_params !== '') { - try { - workflow_engine_params_json = await yaml.load(workflow_engine_params); - workflow_engine_params_json = JSON.stringify( - workflow_engine_params_json - ); - // console.log("workflow_engine_params_json", workflow_engine_params_json); - formData.append( - 'workflow_engine_parameters', - workflow_engine_params_json - ); - } catch (e) { - setShowAdvance(true); - set_workflow_engine_params_error( - 'Workflow engine parameters is not a valid YAML!' - ); - return; - } - } - // workflow_engine_params end - - // workflow_tag - let tags_json = {}; - for (let i = 0; i < tags.length; i++) { - if (tags[i].key === '') { - // eslint-disable-next-line no-var - var temp_tags_error = Array.from({ length: tags.length }, (v, k) => ''); - temp_tags_error[i] = 'Tag key is required!'; - setShowAdvance(true); - set_tags_error(temp_tags_error); - return; - } - if (tags[i].value === '') { - temp_tags_error = Array.from({ length: tags.length }, (v, k) => ''); - temp_tags_error[i] = 'Tag value is required!'; - setShowAdvance(true); - set_tags_error(temp_tags_error); - return; - } - temp_tags_error = Array.from({ length: tags.length }, (v, k) => ''); - set_tags_error(temp_tags_error); - tags_json = Object.assign( - ...tags.map((tag) => ({ [tag.key]: tag.value })) - ); - } - tags_json = JSON.stringify(tags_json); - if (tags.length > 0) { - // console.log("tags", tags_json); - formData.append('tags', tags_json); - } - // workflow_tag end - - try { - // var token = localStorage.getItem("params"); - // token = JSON.parse(token); - // token = token.access_token; - // for (var pair of formData.entries()) { - // console.log(pair[0] + ", " + pair[1]); - // } - const res = await axios.post(`${host_uri_wes}/runs`, formData, { - headers: { - 'content-type': 'multipart/form-data', - Accept: 'application/json', - 'Access-Control-Allow-Origin': '*', - 'Access-Control-Allow-Headers': '*' - // Authorization: `Bearer ${token}`, - } - }); - // showToast("success", "Workflow Added!"); - confirmAlert({ - customUI: ({ onClose }) => { - return ( -
-

- Workflow run added!

- Run Id:{' '} - - {res.data.run_id} - -
Please note the runid.
-

-
- -
-
- ); - } - }); - } catch (e) { - // console.log(e); - showToast('error', 'Server Error!'); - } - }; - - const handleFileRemove = (i) => { - const tempAttachment = workflow_attachments; - tempAttachment.splice(i, 1); - set_workflow_attachments([...tempAttachment]); - }; - - const handleFileRemoveAll = () => { - set_workflow_attachments([]); - }; - - const renderFiles = () => { - if (workflow_attachments.length <= 0) { - return; - } - return ( -
-
    - {workflow_attachments.map((file, i) => ( -
  • -
    - {(() => { - if (file.preview.type === 'image') { - return ; - } else if (file.type === 'application/pdf') { - const fileURL = window.URL.createObjectURL(file); - return ( - - - - ); - } else { - return ( - - - - ); - } - })()} -
    -
    - -
    - {file.name + ' '} -
    -     -
    {file.sizeReadable}
    -
    -
    handleFileRemove(i)} // eslint-disable-line - > - - - -
    -
    • - ))} -
-
handleFileRemoveAll()} // eslint-disable-line - > - - - - Clear All -
-
- ); - }; - - if (isLoggedIn === 'loading') { - return ( -
-
-
- - - - - Loading... -
-
-
- ); - } return ( -
-
-
- {/* dark:text-gray-300 */} - - {/* dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500 */} - -
-
- - {/* dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500 */} - -
-
- - {/* dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500 */} - set_workflow_url(e.target.value)} - value={workflow_url} - placeholder="Please enter valid URL." - /> - {workflow_url_error !== '' ? ( -
{workflow_url_error}
- ) : ( - <> - )} -
{' '} -
- - {/* dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500 */} - set_workflow_params(evn.target.value)} - padding={15} - style={{ - fontFamily: - 'ui-monospace,SFMono-Regular,SF Mono,Consolas,Liberation Mono,Menlo,monospace' - }} - className={`${ - workflow_params_error === '' ? '' : 'border border-red-600' - } bg-100 rounded-lg text-xs w-full block text-gray-900`} - /> - {workflow_params_error !== '' ? ( -
- {workflow_params_error} -
- ) : ( - <> - )} -
-
- -
-
-
setShowAdvance(!showAdvance)} - > -
Advance configurations
-
- {showAdvance ? ( - - - - ) : ( - - - - )} -
-
- {showAdvance ? ( - <> -
- - {/* dark:bg-gray-700 dark:border-gray-600 dark:placeholder-gray-400 dark:text-white dark:focus:ring-blue-500 dark:focus:border-blue-500 */} - - set_workflow_engine_params(evn.target.value) - } - padding={15} - style={{ - fontFamily: - 'ui-monospace,SFMono-Regular,SF Mono,Consolas,Liberation Mono,Menlo,monospace' - }} - className={`${ - workflow_engine_params_error === '' - ? '' - : 'border border-red-600' - } rounded-lg text-xs w-full block text-gray-900`} - /> - {/*