From 9c26d17f58d82d53ff9610461ecd366062301191 Mon Sep 17 00:00:00 2001
From: alilahrime <alahrime@uchicago.edu>
Date: Wed, 17 Aug 2022 10:05:39 -0400
Subject: [PATCH] fix(gwas-ui): fix bugs & pr feedback

---
 src/Analysis/AnalysisApp.jsx                  |  4 +--
 src/Analysis/GWASUIApp/GWASWorkflowList.jsx   |  1 -
 .../shared/CustomDichotomousSelect.jsx        |  2 +-
 .../GWASWizard/shared/GWASFormSubmit.jsx      |  3 +-
 src/Analysis/GWASWizard/shared/GWASJob.jsx    | 31 ++++++++++---------
 .../GWASWizard/shared/WorkflowParameters.jsx  |  2 +-
 src/Analysis/GWASWizard/shared/constants.js   | 10 ++++++
 .../wizardEndpoints/cohortMiddlewareApi.js    |  2 +-
 src/Discovery/Discovery.css                   |  2 +-
 9 files changed, 34 insertions(+), 23 deletions(-)

diff --git a/src/Analysis/AnalysisApp.jsx b/src/Analysis/AnalysisApp.jsx
index 51b8e13c7e..f0a3e71334 100644
--- a/src/Analysis/AnalysisApp.jsx
+++ b/src/Analysis/AnalysisApp.jsx
@@ -225,8 +225,8 @@ class AnalysisApp extends React.Component {
                   ? (
                     <div className='analysis-app__job-status'>
                       {this.isJobRunning() ? <Spin size='large' tip='Job in progress...' /> : null}
-                      {job && job.status === 'Completed' ? <h3>Job Completed</h3> : null}
-                      {job && job.status === 'Failed' ? <h3>Job Failed</h3> : null}
+                      {job?.status === 'Completed' ? <h3>Job Completed</h3> : null}
+                      {job?.status === 'Failed' ? <h3>Job Failed</h3> : null}
                       {results ? results.map((line, i) => <p key={i}>{line}</p>) : null}
                     </div>
                   )
diff --git a/src/Analysis/GWASUIApp/GWASWorkflowList.jsx b/src/Analysis/GWASUIApp/GWASWorkflowList.jsx
index 6f9df04844..a0ab6e6643 100644
--- a/src/Analysis/GWASUIApp/GWASWorkflowList.jsx
+++ b/src/Analysis/GWASUIApp/GWASWorkflowList.jsx
@@ -41,7 +41,6 @@ const GWASWorkflowList = () => {
                 <GWASJob workflow={item} />
               )}
             />
-
           </Panel>
         </Collapse>
       </React.Fragment>
diff --git a/src/Analysis/GWASWizard/shared/CustomDichotomousSelect.jsx b/src/Analysis/GWASWizard/shared/CustomDichotomousSelect.jsx
index a38cd61cbb..9b55931236 100644
--- a/src/Analysis/GWASWizard/shared/CustomDichotomousSelect.jsx
+++ b/src/Analysis/GWASWizard/shared/CustomDichotomousSelect.jsx
@@ -80,7 +80,7 @@ const CustomDichotomousSelect = ({
                 width: 300,
               }}
               actions={[
-                <DeleteOutlined onClick={() => handleCDRemove(cd.uuid)} key='delete' />,
+                <DeleteOutlined onClick={(d) => handleCDRemove(d.uuid)} key='delete' />,
               ]}
             >
               <Meta
diff --git a/src/Analysis/GWASWizard/shared/GWASFormSubmit.jsx b/src/Analysis/GWASWizard/shared/GWASFormSubmit.jsx
index 611d2a132e..73a9849da9 100644
--- a/src/Analysis/GWASWizard/shared/GWASFormSubmit.jsx
+++ b/src/Analysis/GWASWizard/shared/GWASFormSubmit.jsx
@@ -159,7 +159,7 @@ const GWASFormSubmit = ({
 
 GWASFormSubmit.propTypes = {
   sourceId: PropTypes.number.isRequired,
-  outcome: PropTypes.object.isRequired,
+  outcome: PropTypes.object,
   numOfPC: PropTypes.number.isRequired,
   mafThreshold: PropTypes.number.isRequired,
   imputationScore: PropTypes.number.isRequired,
@@ -179,6 +179,7 @@ GWASFormSubmit.defaultProps = {
   selectedControlCohort: undefined,
   selectedCaseCohort: undefined,
   selectedQuantitativeCohort: undefined,
+  outcome: undefined,
 };
 
 export default GWASFormSubmit;
diff --git a/src/Analysis/GWASWizard/shared/GWASJob.jsx b/src/Analysis/GWASWizard/shared/GWASJob.jsx
index ab55e1e706..73c27ce156 100644
--- a/src/Analysis/GWASWizard/shared/GWASJob.jsx
+++ b/src/Analysis/GWASWizard/shared/GWASJob.jsx
@@ -7,14 +7,15 @@ import {
   SyncOutlined,
   CloseCircleOutlined,
   QuestionCircleOutlined,
-  MinusCircleOutlined,
-  StopOutlined,
+  LoadingOutlined,
+  CloseOutlined
 } from '@ant-design/icons';
 import { useQuery } from 'react-query';
 import PropTypes from 'prop-types';
 import { gwasWorkflowPath } from '../../../localconf';
 import { headers } from '../../../configs';
 import { getPresignedUrl } from '../../AnalysisJob';
+import { gwasStatus } from './constants';
 
 const GWASJob = ({ workflow }) => {
   async function handleWorkflowOutput(url) {
@@ -37,16 +38,16 @@ const GWASJob = ({ workflow }) => {
     let buttonText;
     let buttonClickHandler;
 
-    if (phase === 'Succeeded') {
+    if (phase === gwasStatus.suceeded) {
       actionUrl = `${gwasWorkflowPath}status/${workflowName}`;
       buttonText = 'download outputs';
       buttonClickHandler = handleWorkflowOutput;
-    } else if (phase === 'Failed') {
+    } else if (phase === gwasStatus.failed) {
       actionUrl = `${gwasWorkflowPath}logs/${workflowName}`;
       buttonText = 'view logs';
       buttonClickHandler = handleWorkflowLogs;
     }
-    if (['Succeeded', 'Failed'].includes(phase)) {
+    if ([gwasStatus.suceeded, gwasStatus.failed].includes(phase)) {
       actionButtons.unshift(
         <Button
           primary='true'
@@ -75,34 +76,34 @@ const GWASJob = ({ workflow }) => {
       );
     }
     switch (phase) {
-    case 'Running':
+    case gwasStatus.running:
       return (
         <Tag icon={<SyncOutlined spin />} color='processing'>
             In Progress
         </Tag>
       );
-    case 'Succeeded':
+    case gwasStatus.succeeded:
       return (
         <Tag icon={<CheckCircleOutlined />} color='success'>
             Completed
         </Tag>
       );
-    case 'Failed':
+    case gwasStatus.failed:
       return (
         <Tag icon={<CloseCircleOutlined />} color='error'>
             Failed
         </Tag>
       );
-    case 'Canceling':
+    case gwasStatus.pending:
       return (
-        <Tag icon={<MinusCircleOutlined />} color='warning'>
-        Canceling
+        <Tag icon={<LoadingOutlined />} color='processing'>
+            Pending
         </Tag>
       );
-    case 'Canceled':
+    case gwasStatus.error:
       return (
-        <Tag icon={<StopOutlined />} color='warning'>
-        Canceled
+        <Tag icon={<CloseOutlined />} color='error'>
+            Error
         </Tag>
       );
     default:
@@ -144,7 +145,7 @@ const GWASJob = ({ workflow }) => {
             description={(
               <dl>
                 <dt>Workflow Name: {data.wf_name}</dt>
-                <dt>Started at {data.startedAt} and finished at {finishedAt}</dt>
+                <dt>Started at {data.startedAt} {data.phase === gwasStatus.succeeded ? `and finished at ${finishedAt}`: ''}</dt>
               </dl>
             )}
 
diff --git a/src/Analysis/GWASWizard/shared/WorkflowParameters.jsx b/src/Analysis/GWASWizard/shared/WorkflowParameters.jsx
index 5fc3c32c4a..b5983cadfe 100644
--- a/src/Analysis/GWASWizard/shared/WorkflowParameters.jsx
+++ b/src/Analysis/GWASWizard/shared/WorkflowParameters.jsx
@@ -72,7 +72,7 @@ const WorkflowParameters = ({
           <Select
             id='select-dichotomous-covariates'
             mode='multiple'
-            value={selectedDichotomousCovariates.map((s) => s.concept_name)}
+            value={selectedDichotomousCovariates.length ? selectedDichotomousCovariates.map((s) => s.provided_name) : []}
             // TODO currently cant delete cd's from this page
             // onChange={(e) => handleDichotomousCovariateDelete(e)}
             style={{ width: '70%' }}
diff --git a/src/Analysis/GWASWizard/shared/constants.js b/src/Analysis/GWASWizard/shared/constants.js
index 68fed238c2..51f69e1120 100644
--- a/src/Analysis/GWASWizard/shared/constants.js
+++ b/src/Analysis/GWASWizard/shared/constants.js
@@ -1,3 +1,13 @@
+export const hareConceptId = 2000007027;
+
+export const gwasStatus = {
+  pending: 'Pending',
+  running: 'Running',
+  succeeded: 'Succeeded',
+  failed: 'Failed',
+  error: 'Error',
+};
+
 export const quantitativeSteps = [
   {
     title: 'Step 1',
diff --git a/src/Analysis/GWASWizard/wizardEndpoints/cohortMiddlewareApi.js b/src/Analysis/GWASWizard/wizardEndpoints/cohortMiddlewareApi.js
index 1cd1308dbf..0b18633e9f 100644
--- a/src/Analysis/GWASWizard/wizardEndpoints/cohortMiddlewareApi.js
+++ b/src/Analysis/GWASWizard/wizardEndpoints/cohortMiddlewareApi.js
@@ -2,9 +2,9 @@ import { useState, useEffect } from 'react';
 import { cohortMiddlewarePath, wtsPath } from '../../../localconf';
 import { fetchWithCreds } from '../../../actions';
 import { headers } from '../../../configs';
+import { hareConceptId } from '../shared/constants';
 
 export const fetchConceptStatsByHare = async (cohortDefinitionId, selectedCovariates, selectedDichotomousCovariates, sourceId) => {
-  const hareConceptId = 2000007027;
   const variablesPayload = {
     variables:
       [
diff --git a/src/Discovery/Discovery.css b/src/Discovery/Discovery.css
index 4dfba96496..76667b5cab 100644
--- a/src/Discovery/Discovery.css
+++ b/src/Discovery/Discovery.css
@@ -532,7 +532,7 @@
 .discovery-modal__subheading {
   background-color: #dfe3e2;
   border-radius: 4px;
-  padding: 0 10px;
+  padding: 0px 10px;
 }
 
 .discovery-modal__fieldgroup {