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improve search and filter of authorized and unauthorized studies #4614

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improve search and filter of authorized and unauthorized studies #4614

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2f10d41
improve search of authorized and unauthorized studies
jagnathan Feb 15, 2023
e81ef64
Disable keycloak caching for localdb tests
dippindots May 5, 2023
0e11c0b
Merge pull request #4615 from cBioPortal/diable_keycloak_cache
dippindots May 5, 2023
b4a2e5e
improve search of authorized and unauthorized studies
jagnathan Feb 15, 2023
71eca58
Merge branch 'fix-9915-improving-findability' of https://github.com/j…
jagnathan May 5, 2023
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7 changes: 0 additions & 7 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -298,9 +298,6 @@ jobs:
- restore_cache:
keys:
- v10-cbio-database-files-{{ checksum "/tmp/db_data_md5key" }}
- restore_cache:
keys:
- v14-keycloak-database-files-{{ checksum "e2e-localdb-workspace/keycloak/keycloak-config-generated.json" }}
- run:
name: Init database
command: |
Expand All @@ -326,10 +323,6 @@ jobs:
sudo chmod -R 777 $KC_DB_DATA_DIR && \
sudo chown -R circleci:circleci $KC_DB_DATA_DIR; \
fi
- save_cache:
paths:
- /tmp/repo/e2e-localdb-workspace/kc_db_data
key: v14-keycloak-database-files-{{ checksum "e2e-localdb-workspace/keycloak/keycloak-config-generated.json" }}
- run:
name: Run end-2-end tests with studies in local database
command: |
Expand Down
107 changes: 68 additions & 39 deletions src/shared/components/query/CancerStudySelector.tsx
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Expand Up @@ -57,6 +57,9 @@ export default class CancerStudySelector extends React.Component<
onCheckAllFiltered: () => {
this.logic.mainView.toggleAllFiltered();
},
onCheckAuthorizedFiltered: () => {
this.logic.mainView.toggleAllAuthorizedAndFiltered();
},
onClearFilter: () => {
this.store.setSearchText('');
},
Expand Down Expand Up @@ -193,9 +196,16 @@ export default class CancerStudySelector extends React.Component<
shownAndSelectedStudies,
} = this.logic.mainView.getSelectionReport();

const shownAndAuthorizedStudies = shownStudies.filter(study => {
return study.readPermission;
});
const quickSetButtons = this.logic.mainView.quickSelectButtons(
getServerConfig().skin_quick_select_buttons
);
const shownStudiesLengthstring =
shownStudies.length < this.store.cancerStudies.result.length
? 'matching filter'
: '';

return (
<FlexCol
Expand Down Expand Up @@ -307,45 +317,64 @@ export default class CancerStudySelector extends React.Component<
</div>
</Then>
<Else>
<label>
<input
type="checkbox"
data-test="selectAllStudies"
style={{ top: -2 }}
onClick={
this.handlers
.onCheckAllFiltered
}
checked={
shownAndSelectedStudies.length ===
shownStudies.length
}
/>
<strong>
{shownAndSelectedStudies.length ===
shownStudies.length
? `Deselect all listed studies ${
shownStudies.length <
this.store
.cancerStudies
.result.length
? 'matching filter'
: ''
} (${
shownStudies.length
})`
: `Select all listed studies ${
shownStudies.length <
this.store
.cancerStudies
.result.length
? 'matching filter'
: ''
} (${
shownStudies.length
})`}
</strong>
</label>
<If
condition={
getServerConfig()
.skin_home_page_show_unauthorized_studies ===
false
}
>
<Then>
<label>
<input
type="checkbox"
data-test="selectAllStudies"
style={{ top: -2 }}
onClick={
this.handlers
.onCheckAllFiltered
}
checked={
shownAndSelectedStudies.length ===
shownStudies.length
}
/>
<strong>
{shownAndSelectedStudies.length ===
shownStudies.length
? `Deselect all listed studies ${shownStudiesLengthstring} (${shownStudies.length})`
: `Select all listed studies ${shownStudiesLengthstring} (${shownStudies.length})`}
</strong>
</label>
</Then>
<Else>
<label>
<input
type="checkbox"
data-test="selectAuthorizedStudies"
style={{ top: -2 }}
onClick={
this.handlers
.onCheckAuthorizedFiltered
}
checked={
shownAndSelectedStudies.length ===
shownAndAuthorizedStudies.length &&
shownAndAuthorizedStudies.length >
0
}
/>
<strong>
{shownAndSelectedStudies.length ===
shownAndAuthorizedStudies.length &&
shownAndAuthorizedStudies.length >
0
? `Deselect all authorized studies ${shownStudiesLengthstring} (${shownAndAuthorizedStudies.length})`
: `Select all authorized studies ${shownStudiesLengthstring} (${shownAndAuthorizedStudies.length})`}
</strong>
</label>
</Else>
</If>
</Else>
</If>
</If>
Expand Down
12 changes: 11 additions & 1 deletion src/shared/components/query/QueryStore.ts
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Expand Up @@ -129,7 +129,7 @@ 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 @@ -1479,6 +1479,16 @@ 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
36 changes: 36 additions & 0 deletions src/shared/components/query/StudyListLogic.ts
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Expand Up @@ -400,6 +400,42 @@ export class FilteredCancerTreeView {
);
}

@action toggleAllAuthorizedAndFiltered() {
const {
selectableSelectedStudyIds,
selectableSelectedStudies,
shownStudies,
shownAndSelectedStudies,
} = this.getSelectionReport();

let updatedSelectableSelectedStudyIds: string[] = [];
const shownAndAuthorizedStudies = shownStudies.filter(study => {
return study.readPermission;
});
if (
shownAndAuthorizedStudies.length === shownAndSelectedStudies.length
) {
// deselect
updatedSelectableSelectedStudyIds = _.without(
this.store.selectableSelectedStudyIds,
...shownAndAuthorizedStudies.map(
(study: CancerStudy) => study.studyId
)
);
} else {
updatedSelectableSelectedStudyIds = _.union(
this.store.selectableSelectedStudyIds,
shownAndAuthorizedStudies.map(
(study: CancerStudy) => study.studyId
)
);
}

this.store.selectableSelectedStudyIds = updatedSelectableSelectedStudyIds.filter(
id => !_.includes(this.store.deletedVirtualStudies, id)
);
}

@action selectAllMatchingStudies(match: string | string[]) {
const {
selectableSelectedStudyIds,
Expand Down
10 changes: 7 additions & 3 deletions src/shared/components/query/filteredSearch/Phrase.tsx
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Expand Up @@ -129,9 +129,12 @@ export class ListPhrase implements Phrase {
public match(study: FullTextSearchNode): boolean {
let anyFieldMatch = false;
for (const fieldName of this.fields) {
if (!_.has(study, fieldName)) {
continue;
}
let anyPhraseMatch = false;
const fieldValue = study[fieldName];
if (fieldValue) {
if (typeof fieldValue !== 'undefined') {
for (const phrase of this._phraseList) {
anyPhraseMatch =
anyPhraseMatch ||
Expand Down Expand Up @@ -167,7 +170,8 @@ 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 _.toString(toMatch).toLowerCase() === phrase.toLowerCase();
}
12 changes: 10 additions & 2 deletions src/shared/components/query/filteredSearch/field/CheckboxFilterField.spec.ts
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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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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 @@ -43,53 +47,53 @@ 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 @@ -159,7 +163,8 @@ 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))];
} else {
Expand Down
12 changes: 12 additions & 0 deletions src/shared/components/query/filteredSearch/field/FilterFieldOption.ts
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@@ -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;
}
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