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Fix 9915 improving search filter by authorization #4985

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Fix 9915 improving search filter by authorization #4985

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32914dc
Create FilterFieldOption to store search field as displayValue and value
jagnathan Jan 3, 2024
19af8bc
Added study authorization as an option in search filter
jagnathan Jan 4, 2024
389ca12
Add option to search based on authorized and unauthorized studies
jagnathan Jan 10, 2024
987dcca
Merge branch 'cBioPortal:master' into fix-9915-improving-search-filte…
jagnathan Aug 27, 2024
90267c4
Use state from mobx and latest libraries
jagnathan Aug 27, 2024
1636d70
Merge branch 'fix-9915-improving-search-filter-by-authorization-v2' o…
jagnathan Aug 27, 2024
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12 changes: 11 additions & 1 deletion src/shared/components/query/QueryStore.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -151,7 +151,7 @@ export class QueryStore {

@computed
get queryParser() {
return new QueryParser(this.referenceGenomes);
return new QueryParser(this.referenceGenomes, this.readPermissions);
}

initialize(urlWithInitialParams?: string) {
Expand Down Expand Up @@ -1573,6 +1573,16 @@ export class QueryStore {
return new Set(referenceGenomes);
}

@computed get readPermissions(): Set<string> {
const studies = Array.from(this.treeData.map_node_meta.keys()).filter(
s => typeof (s as CancerStudy).readPermission !== 'undefined'
);
const readPermissions = studies.map(n =>
(n as CancerStudy).readPermission.toString()
);
return new Set(readPermissions);
}

@computed get selectableSelectedStudies() {
return this.selectableSelectedStudyIds
.map(
Expand Down
7 changes: 4 additions & 3 deletions src/shared/components/query/filteredSearch/Phrase.tsx
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Expand Up @@ -129,7 +129,7 @@ export class ListPhrase implements Phrase {
for (const fieldName of this.fields) {
let anyPhraseMatch = false;
const fieldValue = study[fieldName];
if (fieldValue) {
if (fieldValue !== undefined) {
for (const phrase of this._phraseList) {
anyPhraseMatch =
anyPhraseMatch ||
Expand Down Expand Up @@ -165,7 +165,8 @@ function matchPhrase(phrase: string, fullText: string) {

/**
* Full match using lowercase
* Need to convert boolean to string before applying lowercase
*/
function matchPhraseFull(phrase: string, fullText: string) {
return fullText.toLowerCase() === phrase.toLowerCase();
function matchPhraseFull(phrase: string, toMatch: boolean | string | number) {
return toMatch.toString().toLowerCase() === phrase.toLowerCase();
}
12 changes: 10 additions & 2 deletions src/shared/components/query/filteredSearch/field/CheckboxFilterField.spec.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,10 @@ import {
} from 'shared/components/query/filteredSearch/field/CheckboxFilterField';
import { CancerTreeSearchFilter } from 'shared/lib/query/textQueryUtils';
import { ListPhrase } from 'shared/components/query/filteredSearch/Phrase';
import {
toFilterFieldOption,
toFilterFieldValue,
} from 'shared/components/query/filteredSearch/field/FilterFieldOption';

describe('CheckboxFilterField', () => {
describe('createQueryUpdate', () => {
Expand All @@ -12,7 +16,7 @@ describe('CheckboxFilterField', () => {
nodeFields: ['studyId'],
form: {
input: FilterCheckbox,
options: ['a', 'b', 'c', 'd', 'e'],
options: ['a', 'b', 'c', 'd', 'e'].map(toFilterFieldOption),
label: 'Test label',
},
} as CancerTreeSearchFilter;
Expand Down Expand Up @@ -48,7 +52,11 @@ describe('CheckboxFilterField', () => {
it('removes all update when only And', () => {
const checked = dummyFilter.form.options;
const toRemove: ListPhrase[] = [];
const result = createQueryUpdate(toRemove, checked, dummyFilter);
const result = createQueryUpdate(
toRemove,
checked.map(toFilterFieldValue),
dummyFilter
);
expect(result.toAdd?.length).toEqual(0);
});

Expand Down
59 changes: 32 additions & 27 deletions src/shared/components/query/filteredSearch/field/CheckboxFilterField.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,15 @@ import {
} from 'shared/lib/query/textQueryUtils';
import { FieldProps } from 'shared/components/query/filteredSearch/field/FilterFormField';
import { ListPhrase } from 'shared/components/query/filteredSearch/Phrase';
import {
FilterFieldOption,
toFilterFieldValue,
} from 'shared/components/query/filteredSearch/field/FilterFieldOption';

export type CheckboxFilterField = {
input: typeof FilterCheckbox;
label: string;
options: string[];
options: FilterFieldOption[];
};

export const FilterCheckbox: FunctionComponent<FieldProps> = props => {
Expand All @@ -40,52 +44,52 @@ export const FilterCheckbox: FunctionComponent<FieldProps> = props => {
}
});
for (const option of options) {
const isChecked = isOptionChecked(option, relevantClauses);
const isChecked = isOptionChecked(option.value, relevantClauses);
if (isChecked) {
checkedOptions.push(option);
checkedOptions.push(option.value);
}
}
return (
<div className="filter-checkbox">
<h5>{props.filter.form.label}</h5>
<div>
{options.map((option: string) => {
const id = `input-${option}`;
let isChecked = checkedOptions.includes(option);
{options.map((option: FilterFieldOption) => {
const id = `input-${option.displayValue}-${option.value}`;
let isChecked = checkedOptions.includes(option.value);
return (
<div
style={{
display: 'inline-block',
padding: '0 1em 0 0',
}}
>
<input
type="checkbox"
id={id}
value={option}
checked={isChecked}
onClick={() => {
isChecked = !isChecked;
updatePhrases(option, isChecked);
const update = createQueryUpdate(
toRemove,
checkedOptions,
props.filter
);
props.onChange(update);
}}
style={{
display: 'inline-block',
}}
/>
<label
htmlFor={id}
style={{
display: 'inline-block',
padding: '0 0 0 0.2em',
}}
>
{option}
<input
type="checkbox"
id={id}
value={option.displayValue}
checked={isChecked}
onClick={() => {
isChecked = !isChecked;
updatePhrases(option.value, isChecked);
const update = createQueryUpdate(
toRemove,
checkedOptions,
props.filter
);
props.onChange(update);
}}
style={{
display: 'inline-block',
}}
/>{' '}
{option.displayValue}
</label>
</div>
);
Expand Down Expand Up @@ -152,7 +156,8 @@ export function createQueryUpdate(
toAdd = [];
} else if (onlyNot || moreAnd) {
const phrase = options
.filter(o => !optionsToAdd.includes(o))
.filter(o => !optionsToAdd.includes(o.value))
.map(toFilterFieldValue)
.join(FILTER_VALUE_SEPARATOR);

toAdd = [new NotSearchClause(createListPhrase(prefix, phrase, fields))];
Expand Down
12 changes: 12 additions & 0 deletions src/shared/components/query/filteredSearch/field/FilterFieldOption.ts
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Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
export type FilterFieldOption = {
value: string;
displayValue: string;
};

export function toFilterFieldOption(option: string) {
return { value: option, displayValue: option };
}

export function toFilterFieldValue(option: FilterFieldOption) {
return option.value;
}
8 changes: 4 additions & 4 deletions src/shared/components/query/filteredSearch/field/ListFormField.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -5,22 +5,22 @@ import { SearchClause } from 'shared/components/query/filteredSearch/SearchClaus
import { Phrase } from 'shared/components/query/filteredSearch/Phrase';
import './ListFormField.scss';
import { toQueryString } from 'shared/lib/query/textQueryUtils';
import { FilterFieldOption } from 'shared/components/query/filteredSearch/field/FilterFieldOption';

export type ListFilterField = {
label: string;
input: typeof FilterList;
options: string[];
options: FilterFieldOption[];
};

export const FilterList: FunctionComponent<FieldProps> = props => {
const form = props.filter.form as ListFilterField;
const allPhrases = toUniquePhrases(props.query);
const queryString = toQueryString(props.query);
return (
<div className="filter-list">
<h5>{props.filter.form.label}</h5>
{form.options.map(option => {
const update = props.parser.parseSearchQuery(option);
const update = props.parser.parseSearchQuery(option.value);
return (
<li className="dropdown-item">
<a
Expand All @@ -32,7 +32,7 @@ export const FilterList: FunctionComponent<FieldProps> = props => {
});
}}
>
{option}
{option.displayValue}
</a>
</li>
);
Expand Down
60 changes: 53 additions & 7 deletions src/shared/components/unknownStudies/UnknownStudiesWarning.tsx
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@@ -1,26 +1,72 @@
import * as React from 'react';
import { observer } from 'mobx-react';
import { Collapse } from 'react-collapse';
import classnames from 'classnames';
import { action, computed, observable, makeObservable } from 'mobx';


@observer
export default class UnknownStudiesWarning extends React.Component<
{ ids: String[] },
{ studiesCollapsed: boolean },
{}
> {
constructor(props: { ids: String[] }) {
super(props);
this.state = {
studiesCollapsed: true
};
}

@observable studiesCollapsed = false;

@action.bound
toggleStudiesCollapse() {
this.studiesCollapsed = !this.studiesCollapsed;
}

render() {
const { studiesCollapsed } = this.state;
if (this.props.ids.length > 0) {
return (
<div
className="alert alert-danger"
data-test="unkown-study-warning"
style={{ marginBottom: 0 }}
>
<i className="fa fa-exclamation-triangle"></i> The following
studies do not exist or you do not have access to them:
<ul style={{ margin: '10px 0' }}>
{this.props.ids.map(id => (
<li>{id}</li>
))}
</ul>

<div
style={{
display: 'flex',
alignItems: 'center',
}}
onClick={() => this.toggleStudiesCollapse()}
>
<i className="fa fa-exclamation-triangle"></i> The following
studies do not exist or you do not have access to them.
<span style={{ float: 'right' }}>
{studiesCollapsed ? (
<i
className={classnames(
'fa fa-chevron-down'
)}
/>
) : (
<i
className={classnames(
'fa fa-chevron-up'
)}
/>
)}
</span>
</div>
<Collapse isOpened={!studiesCollapsed}>
<ul style={{ margin: '10px 0' }}>
{this.props.ids.map(id => (
<li>{id}</li>
))}
</ul>
</Collapse>
Please resubmit your query below.
</div>
);
Expand Down
2 changes: 1 addition & 1 deletion src/shared/lib/query/QueryParser.spec.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ import { QueryParser } from 'shared/lib/query/QueryParser';
import { StringPhrase } from 'shared/components/query/filteredSearch/Phrase';

describe('QueryParser', () => {
const parser = new QueryParser(new Set<string>());
const parser = new QueryParser(new Set<string>(), new Set<string>());
const referenceGenomeFields = parser.searchFilters.find(
f => f.phrasePrefix === 'reference-genome'
)!.nodeFields;
Expand Down
28 changes: 25 additions & 3 deletions src/shared/lib/query/QueryParser.ts
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Expand Up @@ -18,14 +18,15 @@ import {
ListPhrase,
Phrase,
} from 'shared/components/query/filteredSearch/Phrase';
import { toFilterFieldOption } from 'shared/components/query/filteredSearch/field/FilterFieldOption';

export class QueryParser {
/**
* Can be extended with additional search filters
*/
private readonly _searchFilters: CancerTreeSearchFilter[];

constructor(referenceGenomes: Set<string>) {
constructor(referenceGenomes: Set<string>, readPermissions: Set<string>) {
this._searchFilters = [
/**
* Example queries:
Expand All @@ -38,7 +39,7 @@ export class QueryParser {
input: FilterList,
options: ServerConfigHelpers.skin_example_study_queries(
getServerConfig()!.skin_example_study_queries || ''
),
).map(toFilterFieldOption),
},
},
/**
Expand All @@ -49,10 +50,31 @@ export class QueryParser {
nodeFields: ['referenceGenome'],
form: {
input: FilterCheckbox,
options: [...referenceGenomes],
options: [...referenceGenomes].map(toFilterFieldOption),
label: 'Reference genome',
},
},
/**
* Show Authorized Studies
*/
{
phrasePrefix: 'authorized',
nodeFields: ['readPermission'],
form: {
input: FilterCheckbox,
options:
readPermissions.size > 1
? [
{ value: 'true', displayValue: 'Authorized' },
{
value: 'false',
displayValue: 'Unauthorized',
},
]
: [],
label: 'Controlled access',
},
},
];
}

Expand Down
2 changes: 1 addition & 1 deletion src/shared/lib/query/textQueryUtils.spec.ts
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Expand Up @@ -15,7 +15,7 @@ import { QueryParser } from 'shared/lib/query/QueryParser';
import { StringPhrase } from 'shared/components/query/filteredSearch/Phrase';

describe('textQueryUtils', () => {
const parser = new QueryParser(new Set<string>());
const parser = new QueryParser(new Set<string>(), new Set<string>());
const referenceGenomeFields = parser.searchFilters.find(
f => f.phrasePrefix === 'reference-genome'
)!.nodeFields;
Expand Down
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