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Study View: Always show selected genes on top and alterante selected …
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…rows color
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@kalletlak
kalletlak committed Jan 16, 2020
1 parent 145fb82 commit ea09d84
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Showing 5 changed files with 115 additions and 99 deletions.
12 changes: 6 additions & 6 deletions src/pages/studyView/StudyViewPageStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -1603,16 +1603,16 @@ export class StudyViewPageStore {

}

public getMutatedGenesTableFilters(): string[] {
return _.flatMap(this._mutatedGeneFilter, filter => filter.entrezGeneIds).map(entrezGeneId => getMutationUniqueKey(entrezGeneId, this.geneMapCache[entrezGeneId]));
public getMutatedGenesTableFilters() {
return _.map(this._mutatedGeneFilter, filter => filter.entrezGeneIds.map(entrezGeneId => getMutationUniqueKey(entrezGeneId, this.geneMapCache[entrezGeneId])));
}

public getFusionGenesTableFilters(): string[] {
return _.flatMap(this._fusionGeneFilter, filter => filter.entrezGeneIds).map(entrezGeneId => getMutationUniqueKey(entrezGeneId, this.geneMapCache[entrezGeneId]));
public getFusionGenesTableFilters() {
return _.map(this._fusionGeneFilter, filter => filter.entrezGeneIds.map(entrezGeneId => getMutationUniqueKey(entrezGeneId, this.geneMapCache[entrezGeneId])));
}

public getCNAGenesTableFilters(): string[] {
return _.flatMap(this._cnaGeneFilter, filter => filter.alterations).map(alteration => getCnaUniqueKey(alteration.entrezGeneId, this.geneMapCache[alteration.entrezGeneId], alteration.alteration));
public getCNAGenesTableFilters() {
return _.map(this._cnaGeneFilter, filter => filter.alterations.map(alteration => getCnaUniqueKey(alteration.entrezGeneId, this.geneMapCache[alteration.entrezGeneId], alteration.alteration)));
}

public getClinicalDataFiltersByUniqueKey(uniqueKey: string): string[] {
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15 changes: 0 additions & 15 deletions src/pages/studyView/TableUtils.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@ import {
CopyNumberAlterationIdentifier
} from "pages/studyView/StudyViewPageStore";
import * as _ from "lodash";
import {GeneTableUserSelectionWithIndex} from "pages/studyView/table/GeneTable";

export type AlteredGenesTableUserSelectionWithIndex = {
entrezGeneId: number;
Expand Down Expand Up @@ -117,17 +116,3 @@ export function getFreqColumnRender(type: FreqColumnType, numberOfProfiledCases:
</DefaultTooltip>
);
}

export function rowIsChecked(uniqueKey: string, preSelectedRows: GeneTableUserSelectionWithIndex[], selectedRows: GeneTableUserSelectionWithIndex[]) {
return _.some(
preSelectedRows.concat(selectedRows),
(row: GeneTableUserSelectionWithIndex) => row.uniqueKey === uniqueKey
);
};

export function rowIsDisabled(uniqueKey: string, selectedRows: GeneTableUserSelectionWithIndex[]) {
return _.some(
selectedRows,
(row: GeneTableUserSelectionWithIndex) => row.uniqueKey === uniqueKey
);
};
54 changes: 47 additions & 7 deletions src/pages/studyView/table/FixedHeaderTable.tsx
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
import * as React from "react";
import {Column, LazyMobXTableStore, SortDirection} from "../../../shared/components/lazyMobXTable/LazyMobXTable";
import {Column, LazyMobXTableStore, SortDirection, lazyMobXTableSort} from "../../../shared/components/lazyMobXTable/LazyMobXTable";
import {
Column as RVColumn,
SortDirection as RVSortDirection,
Expand All @@ -17,9 +17,11 @@ import {If} from 'react-if';
import autobind from 'autobind-decorator';
import {inputBoxChangeTimeoutEvent} from "../../../shared/lib/EventUtils";
import {DefaultTooltip} from "cbioportal-frontend-commons";
import { SimpleGetterLazyMobXTableApplicationDataStore } from "shared/lib/ILazyMobXTableApplicationDataStore";

export type IFixedHeaderTableProps<T> = {
columns: Column<T>[],
fixedTopRowsData?: T[];
data: T[];
sortBy?: string;
sortDirection?: SortDirection;
Expand All @@ -38,6 +40,7 @@ export type IFixedHeaderTableProps<T> = {
removeAllDisabled?:boolean;
showSelectableNumber?: boolean;
isSelectedRow?: (data: T) => boolean;
highlightedRowClassName?: (data: T) => string;
autoFocusSearchAfterRendering?:boolean;
afterSorting?: (sortBy: string, sortDirection: SortDirection) => void;
};
Expand All @@ -47,6 +50,24 @@ const RVSDTtoStrType = {
['asc' as SortDirection]: RVSortDirection.ASC
};

export class FixedHeaderTableDataStore extends SimpleGetterLazyMobXTableApplicationDataStore<any> {

constructor(getData: () => any[], fixedTopRowsData: any[]) {
super(getData);
this.fixedTopRowsData = fixedTopRowsData;
}

@observable private fixedTopRowsData: any[];

@computed get sortedData() {
// if not defined, use default values for sortMetric and sortAscending
const sortMetric = this.sortMetric || (() => 0);
const sortAscending = this.sortAscending !== undefined ? this.sortAscending : true;

return [...this.fixedTopRowsData, ...lazyMobXTableSort(this.allData, sortMetric, sortAscending)];
}
}

@observer
export default class FixedHeaderTable<T> extends React.Component<IFixedHeaderTableProps<T>, {}> {
private _store: LazyMobXTableStore<T>;
Expand Down Expand Up @@ -78,32 +99,51 @@ export default class FixedHeaderTable<T> extends React.Component<IFixedHeaderTab
this.initDataStore();
}

componentWillReceiveProps(nextProps: any) {
componentWillReceiveProps(nextProps: IFixedHeaderTableProps<T>) {
this.updateDataStore(nextProps);
}

updateDataStore(nextProps: any) {
updateDataStore(nextProps: IFixedHeaderTableProps<T>) {
const tableDataStore = new FixedHeaderTableDataStore(
() => {
return this.props.data;
},
this.props.fixedTopRowsData || []
);
this._store.setProps({
columns: nextProps.columns,
data: nextProps.data,
dataStore: tableDataStore,
initialSortColumn: this._sortBy,
initialSortDirection: this._sortDirection
});
}

initDataStore() {
const tableDataStore = new FixedHeaderTableDataStore(
() => {
return this.props.data;
},
this.props.fixedTopRowsData || []
);
this._store = new LazyMobXTableStore<T>({
columns: this.props.columns,
data: this.props.data,
dataStore: tableDataStore,
initialSortColumn: this._sortBy,
initialSortDirection: this._sortDirection
});
}

@autobind
rowClassName({index}: any) {
rowClassName({ index }: any) {
if (index > -1 && this.isSelectedRow(this._store.dataStore.sortedFilteredData[index])) {
return classnames(styles.row, styles.highlightedRow);
const classNames: string[] = [styles.row]
if (this.props.highlightedRowClassName) {
const className = this.props.highlightedRowClassName(this._store.dataStore.sortedFilteredData[index]);
classNames.push(className);
} else {
classNames.push(styles.highlightedRow);
}
return classnames(classNames);
} else if (index < 0) {
return styles.headerRow;
} else {
Expand Down
127 changes: 57 additions & 70 deletions src/pages/studyView/table/GeneTable.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -17,16 +17,13 @@ import {
import {
OncokbCancerGene
} from "pages/studyView/StudyViewPageStore";
import {getFreqColumnRender, getGeneColumnHeaderRender, rowIsChecked, rowIsDisabled} from "pages/studyView/TableUtils";
import {getFreqColumnRender, getGeneColumnHeaderRender} from "pages/studyView/TableUtils";
import {GeneCell} from "pages/studyView/table/GeneCell";
import LabeledCheckbox from "shared/components/labeledCheckbox/LabeledCheckbox";
import styles from "pages/studyView/table/tables.module.scss";
import MobxPromise from "mobxpromise";

export type GeneTableUserSelectionWithIndex = {
uniqueKey: string;
rowIndex: number;
};
import { stringListToIndexSet } from "cbioportal-frontend-commons";
import ifNotDefined from "shared/lib/ifNotDefined";

export type GeneTableRow = OncokbCancerGene & {
entrezGeneId: number
Expand Down Expand Up @@ -61,7 +58,7 @@ export type GeneTableProps = & {
promise: MobxPromise<GeneTableRow[]>;
width: number;
height: number;
filters: string[];
filters: string[][];
onUserSelection: (value: string[]) => void;
numOfSelectedSamples: number;
onGeneSelect: (hugoGeneSymbol: string) => void;
Expand Down Expand Up @@ -89,7 +86,7 @@ class GeneTableComponent extends FixedHeaderTable<GeneTableRow> {

@observer
export class GeneTable extends React.Component<GeneTableProps, {}> {
@observable protected preSelectedRows: GeneTableUserSelectionWithIndex[] = [];
@observable protected selectedRowsKeys: string[] = [];
@observable protected sortBy: GeneTableColumnKey;
@observable private sortDirection: SortDirection;
@observable private modalSettings: {
Expand Down Expand Up @@ -367,12 +364,39 @@ export class GeneTable extends React.Component<GeneTableProps, {}> {
return this.isFilteredByCancerGeneList ? _.filter(this.props.promise.result, data => data.isCancerGene) : (this.props.promise.result || []);
}

@computed get flattenedFilters() {
return _.flatMap(this.props.filters);
}

@computed get selectableTableData() {
if (this.flattenedFilters.length === 0) {
return this.tableData;
}
return _.filter(this.tableData, data => !this.flattenedFilters.includes(data.uniqueKey));
}

@computed
get preSelectedRows() {
if (this.flattenedFilters.length === 0) {
return [];
}
const order = stringListToIndexSet(this.flattenedFilters);
return _.chain(this.tableData)
.filter(data => this.flattenedFilters.includes(data.uniqueKey))
.sortBy<GeneTableRow>(data => ifNotDefined(order[data.uniqueKey], Number.POSITIVE_INFINITY))
.value();
}

@computed
get preSelectedRowsKeys() {
return this.preSelectedRows.map(row => row.uniqueKey);
}

@computed
get tableColumns() {
return this.props.columns.map(column => this.getDefaultColumnDefinition(column.columnKey, this.columnsWidth[column.columnKey], this.cellMargin[column.columnKey]));
}


@autobind
@action
toggleModal(panelName: string) {
Expand All @@ -399,88 +423,49 @@ export class GeneTable extends React.Component<GeneTableProps, {}> {
return !!this.props.cancerGeneFilterEnabled && this.props.filterByCancerGenes;
}

@computed get allSelectedRowsKeys() {
return [...this.selectedRowsKeys, ...this.preSelectedRowsKeys];
}

@autobind
isChecked(uniqueKey: string) {
return rowIsChecked(uniqueKey, this.preSelectedRows, this.selectedRows);
return _.some(this.allSelectedRowsKeys, (key) => key === uniqueKey);
}

@autobind
isDisabled(uniqueKey: string) {
return rowIsDisabled(uniqueKey, this.selectedRows);
return _.some(this.preSelectedRowsKeys, (key) => key === uniqueKey);
}

@autobind
togglePreSelectRow(uniqueKey: string) {
const record: GeneTableUserSelectionWithIndex | undefined = _.find(
this.preSelectedRows,
(row: GeneTableUserSelectionWithIndex) => row.uniqueKey === uniqueKey
);
const record = _.find(this.selectedRowsKeys,(key) => key === uniqueKey);
if (_.isUndefined(record)) {
let dataIndex = -1;
// definitely there is a match
const datum = _.find(
this.tableData,
(row, index: number) => {
const exist = row.uniqueKey! === uniqueKey;
if (exist) {
dataIndex = index;
}
return exist;
}
);

if (!_.isUndefined(datum)) {
this.preSelectedRows.push({
rowIndex: dataIndex,
uniqueKey: datum.uniqueKey!,
});
}
this.selectedRowsKeys.push(uniqueKey);
} else {
this.preSelectedRows = _.xorBy(this.preSelectedRows, [record], "rowIndex");
this.selectedRowsKeys = _.xorBy(this.selectedRowsKeys, [record]);
}
}

@autobind
@action
afterSelectingRows() {
this.props.onUserSelection(
this.preSelectedRows.map(row => row.uniqueKey)
);
this.preSelectedRows = [];
this.props.onUserSelection(this.selectedRowsKeys);
this.selectedRowsKeys = [];
}

@computed
get selectedRows() {
if (this.props.filters.length === 0) {
return [];
} else {
return _.reduce(
this.tableData,
(
acc: GeneTableUserSelectionWithIndex[],
row,
index: number
) => {
if (_.includes(this.props.filters, row.uniqueKey)) {
acc.push({
rowIndex: index,
uniqueKey: row.uniqueKey
});
}
return acc;
},
[]
);
}
@autobind
isSelectedRow(data: GeneTableRow) {
return this.isChecked(data.uniqueKey);
}

@autobind
isSelectedRow(data: GeneTableRow) {
return !_.isUndefined(
_.find(_.union(this.selectedRows, this.preSelectedRows), function (row) {
return row.uniqueKey === data.uniqueKey;
})
);
selectedRowClassName(data: GeneTableRow) {
const index = _.findIndex(this.props.filters, filter => filter.includes(data.uniqueKey));
if (index === -1) {
return this.props.filters.length % 2 === 0 ? styles.highlightedEvenRow : styles.highlightedOddRow;
}
return index % 2 === 0 ? styles.highlightedEvenRow : styles.highlightedOddRow;
}

@autobind
Expand All @@ -498,14 +483,16 @@ export class GeneTable extends React.Component<GeneTableProps, {}> {
<GeneTableComponent
width={this.props.width}
height={this.props.height}
data={this.tableData}
data={this.selectableTableData}
columns={this.tableColumns}
showSelectSamples={true && this.preSelectedRows.length > 0}
showSelectSamples={true && this.selectedRowsKeys.length > 0}
isSelectedRow={this.isSelectedRow}
afterSelectingRows={this.afterSelectingRows}
sortBy={this.sortBy}
sortDirection={this.sortDirection}
afterSorting={this.afterSorting}
fixedTopRowsData={this.preSelectedRows}
highlightedRowClassName={this.selectedRowClassName}
/>
)}
{this.props.genePanelCache ? (
Expand Down
6 changes: 5 additions & 1 deletion src/pages/studyView/table/tables.module.scss
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Original file line number Diff line number Diff line change
Expand Up @@ -67,10 +67,14 @@ $study-view-table-icon-size: 10px;
background-color: #ffffff;
}

.highlightedRow {
.highlightedEvenRow, .highlightedRow {
background-color: #d3d3d3;
}

.highlightedOddRow {
background-color: #e0e0e0;
}

.cancerGeneIcon {
margin-right: 5px;
}
Expand Down

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