From c3cce60cca215f9a29848466d027d961232f9a54 Mon Sep 17 00:00:00 2001
From: Qi-Xuan Lu <qlu@carisls.com>
Date: Thu, 18 Jan 2024 15:10:43 -0500
Subject: [PATCH] fix pilltags, apis, and select

---
 .../src/generated/CBioPortalAPIInternal.ts    |  4 +-
 src/pages/studyView/UserSelections.tsx        | 63 ++++++++++---------
 .../geneLevelSelection/GeneLevelSelection.tsx | 36 ++++++-----
 src/pages/studyView/tabs/SummaryTab.tsx       |  5 +-
 4 files changed, 61 insertions(+), 47 deletions(-)

diff --git a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts
index 79889c7c184..a56a6560e51 100644
--- a/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts
+++ b/packages/cbioportal-ts-api-client/src/generated/CBioPortalAPIInternal.ts
@@ -4559,7 +4559,7 @@ export default class CBioPortalAPIInternal {
         $queryParameters ? : any
     }): string {
         let queryParameters: any = {};
-        let path = '/mutation-data-counts/fetch';
+        let path = '/api/mutation-data-counts/fetch';
 
         if (parameters.$queryParameters) {
             Object.keys(parameters.$queryParameters).forEach(function(parameterName) {
@@ -4585,7 +4585,7 @@ export default class CBioPortalAPIInternal {
         const domain = parameters.$domain ? parameters.$domain : this.domain;
         const errorHandlers = this.errorHandlers;
         const request = this.request;
-        let path = '/mutation-data-counts/fetch';
+        let path = '/api/mutation-data-counts/fetch';
         let body: any;
         let queryParameters: any = {};
         let headers: any = {};
diff --git a/src/pages/studyView/UserSelections.tsx b/src/pages/studyView/UserSelections.tsx
index d6763d23024..17a75a217ea 100644
--- a/src/pages/studyView/UserSelections.tsx
+++ b/src/pages/studyView/UserSelections.tsx
@@ -1,5 +1,5 @@
 import * as React from 'react';
-import _ from 'lodash';
+import _, { filter } from 'lodash';
 import { observer } from 'mobx-react';
 import { computed, makeObservable, runInAction } from 'mobx';
 import styles from './styles.module.scss';
@@ -302,37 +302,42 @@ export default class UserSelections extends React.Component<
                 );
                 const chartMeta = this.props.attributesMetaSet[uniqueKey];
                 if (chartMeta) {
+                    const filters = mutationDataFilter.values.map(
+                        dataFilterValues => {
+                            return (
+                                <GroupLogic
+                                    components={[
+                                        this.groupedMutationDataFilters(
+                                            dataFilterValues,
+                                            this.props.updateMutationDataFilter,
+                                            chartMeta
+                                        ),
+                                    ]}
+                                    operation=":"
+                                    group={dataFilterValues.length > 1}
+                                />
+                            );
+                        }
+                    );
+
                     acc.push(
                         <div className={styles.parentGroupLogic}>
                             <GroupLogic
-                                components={mutationDataFilter.values.map(
-                                    dataFilterValues => {
-                                        return (
-                                            <GroupLogic
-                                                components={[
-                                                    <span
-                                                        className={
-                                                            styles.filterClinicalAttrName
-                                                        }
-                                                    >
-                                                        {chartMeta.displayName}
-                                                    </span>,
-                                                    this.groupedMutationDataFilters(
-                                                        dataFilterValues,
-                                                        this.props
-                                                            .updateMutationDataFilter,
-                                                        chartMeta
-                                                    ),
-                                                ]}
-                                                operation=":"
-                                                group={
-                                                    dataFilterValues.length > 1
-                                                }
-                                            />
-                                        );
-                                    }
-                                )}
-                                operation={'and'}
+                                components={[
+                                    <span
+                                        className={
+                                            styles.filterClinicalAttrName
+                                        }
+                                    >
+                                        {chartMeta.displayName}
+                                    </span>,
+                                    <GroupLogic
+                                        components={filters}
+                                        operation={'and'}
+                                        group={filters.length > 1}
+                                    />,
+                                ]}
+                                operation={':'}
                                 group={false}
                             />
                         </div>
diff --git a/src/pages/studyView/addChartButton/geneLevelSelection/GeneLevelSelection.tsx b/src/pages/studyView/addChartButton/geneLevelSelection/GeneLevelSelection.tsx
index 647a97507c4..33d06ee042d 100644
--- a/src/pages/studyView/addChartButton/geneLevelSelection/GeneLevelSelection.tsx
+++ b/src/pages/studyView/addChartButton/geneLevelSelection/GeneLevelSelection.tsx
@@ -265,7 +265,8 @@ export default class GeneLevelSelection extends React.Component<
                         <div
                             style={{
                                 flex: 1,
-                                marginRight: 15,
+                                width: '50%',
+                                marginRight: '5%',
                             }}
                         >
                             <ReactSelect
@@ -274,31 +275,36 @@ export default class GeneLevelSelection extends React.Component<
                                 options={this.molecularProfileOptions}
                                 isClearable={false}
                                 isSearchable={false}
+                                style={{ width: '100%' }}
                             />
-                            {this.selectedOption &&
-                                this.subOptions
-                                    .map(option => option.profileType)
-                                    .includes(
-                                        this.selectedOption.alterationType
-                                    ) && (
-                                    <ReactSelect
-                                        value={this.selectedSubOption}
-                                        onChange={this.handleSubSelect}
-                                        options={this.subOptions}
-                                        isClearable={false}
-                                        isSearchable={false}
-                                    />
-                                )}
                         </div>
                         <button
                             disabled={this.isQueryInvalid || this.hasOQL}
                             className="btn btn-primary btn-sm"
                             data-test="GeneLevelSelectionSubmitButton"
                             onClick={this.onAddChart}
+                            style={{ width: '25%' }}
                         >
                             {this.props.submitButtonText}
                         </button>
                     </div>
+                    <div style={{ width: '70%', marginTop: '5px' }}>
+                        {this.selectedOption &&
+                            this.subOptions
+                                .map(option => option.profileType)
+                                .includes(
+                                    this.selectedOption.alterationType
+                                ) && (
+                                <ReactSelect
+                                    value={this.selectedSubOption}
+                                    onChange={this.handleSubSelect}
+                                    options={this.subOptions}
+                                    isClearable={false}
+                                    isSearchable={false}
+                                />
+                            )}
+                    </div>
+
                     {/* <div className={styles.operations}>
                         
                     </div> */}
diff --git a/src/pages/studyView/tabs/SummaryTab.tsx b/src/pages/studyView/tabs/SummaryTab.tsx
index f66022453be..f689ec22bd0 100644
--- a/src/pages/studyView/tabs/SummaryTab.tsx
+++ b/src/pages/studyView/tabs/SummaryTab.tsx
@@ -180,7 +180,10 @@ export class StudySummaryTab extends React.Component<
                 commonProps: () => ({
                     onChangeChartType: this.handlers.onChangeChartType,
                     getData: (dataType?: DataType) =>
-                        this.store.getChartDownloadableData(chartMeta, dataType),
+                        this.store.getChartDownloadableData(
+                            chartMeta,
+                            dataType
+                        ),
                     downloadTypes: ['Summary Data', 'Full Data', 'SVG', 'PDF'],
                 }),
                 [ChartMetaDataTypeEnum.CUSTOM_DATA]: () => ({