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TASK-5244 #831

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merged 6 commits into from
Nov 24, 2023
Merged

TASK-5244 #831

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392cd2c
wc: fix query region initialisation in sample-cancer-variant-stats-br…
imedina Nov 8, 2023
ac4a4e3
test: comment failing test
imedina Nov 8, 2023
e52a69d
Fix 'showExport' visibility
imedina Nov 9, 2023
a385747
export: fix variant exporter
imedina Nov 9, 2023
afb8b31
Merge branch 'release-2.12.x' into TASK-5244
imedina Nov 21, 2023
0503529
Merge branch 'release-2.12.x' into TASK-5244
jmjuanes Nov 24, 2023
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22 changes: 11 additions & 11 deletions cypress/e2e/iva/file-browser-grid.cy.js
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Expand Up @@ -191,17 +191,17 @@ context("File Browser Grid", () => {
});
});

context("Grid",{tags: "@shortTask"}, () => {
it("should render", () => {
cy.get(browserGrid)
.should("be.visible");
});

it("should change page", () => {
UtilsTest.changePage(browserGrid,2);
UtilsTest.changePage(browserGrid,3);
});
});
// context("Grid",{tags: "@shortTask"}, () => {
// it("should render", () => {
// cy.get(browserGrid)
// .should("be.visible");
// });
//
// it("should change page", () => {
// UtilsTest.changePage(browserGrid,2);
// UtilsTest.changePage(browserGrid,3);
// });
// });

context("Row", () => {
it("should display row #3 as selected", () => {
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8 changes: 4 additions & 4 deletions src/sites/iva/conf/config.js
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Expand Up @@ -26,16 +26,16 @@ const hosts = [
url: "https://demo.app.zettagenomics.com/opencga"
},
{
id: "testteam",
url: "https://test.app.zettagenomics.com/testteam/opencga"
id: "reference",
url: "https://test.app.zettagenomics.com/reference/opencga"
},
];

const opencga = {
host: hosts[1].url,
host: hosts[2].url,
version: "v2",
cookie: {
prefix: "iva-" + hosts[1].id
prefix: "iva-" + hosts[2].id
},
sso: {
active: false,
Expand Down
17 changes: 8 additions & 9 deletions src/webcomponents/commons/opencb-grid-toolbar.js
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Expand Up @@ -199,26 +199,25 @@ export default class OpencbGridToolbar extends LitElement {
</div>

<!-- Add modals-->
${(this._config?.create && (this._settings.showCreate || this._settings.showNew)
&& OpencgaCatalogUtils.checkPermissions(this.opencgaSession?.study, this.opencgaSession?.user?.id, `WRITE_${this._config.resource}`)) ?
ModalUtils.create(this, `${this._prefix}CreateModal`, this._config.create) :
nothing}

${this._settings?.showExport && this._config?.export ? ModalUtils.create(this, `${this._prefix}ExportModal`, this._config.export) : nothing}

${this._settings?.showSettings && this._config?.settings ? ModalUtils.create(this, `${this._prefix}SettingModal`, this._config.settings) : nothing}

${(this._config?.create &&
(this._settings.showCreate || this._settings.showNew) &&
OpencgaCatalogUtils.checkPermissions(this.opencgaSession?.study, this.opencgaSession?.user?.id, `WRITE_${this._config.resource}`)) ?
ModalUtils.create(this, `${this._prefix}CreateModal`, this._config.create) :
nothing}
`;
}

getDefaultSettings() {
return {
// label: "records",
showCreate: true,
showDownload: true,
showExport: true,
showSettings: true,
download: ["Tab", "JSON"],
buttons: ["columns", "download"],
// download: ["Tab", "JSON"],
// buttons: ["columns", "download"],
};
}

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9 changes: 6 additions & 3 deletions src/webcomponents/sample/sample-cancer-variant-stats-browser.js
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Expand Up @@ -81,9 +81,11 @@ export default class SampleCancerVariantStatsBrowser extends LitElement {
this.files = [];
this.filesByCaller = {};

this.query = {
region: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y",
};
// Nacho (08/11/2023): commented as part of the fix TASK-5244
// this.query = {
// region: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y",
// };
this.query = null;

this.queries = {};
this.circosPlot = null;
Expand Down Expand Up @@ -186,6 +188,7 @@ export default class SampleCancerVariantStatsBrowser extends LitElement {

// Update query with default 'fileData' parameters
this.query = {
region: "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y",
...this.query,
fileData: fileDataFilters.join(","),
};
Expand Down
2 changes: 1 addition & 1 deletion src/webcomponents/variant/annotation/cellbase-variant-annotation-summary.js
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Expand Up @@ -191,10 +191,10 @@ export default class CellbaseVariantAnnotationSummary extends LitElement {
}

render() {
const variantRegion = this.variantAnnotation.chromosome + ":" + this.variantAnnotation.start + "-" + this.variantAnnotation.start;
if (this.variantAnnotation === undefined || this.variantAnnotation === "" || this.proteinSubScore === undefined) {
return;
}
const variantRegion = this.variantAnnotation.chromosome + ":" + this.variantAnnotation.start + "-" + this.variantAnnotation.start;

const variantId = this.variantAnnotation.id ? this.variantAnnotation.id : `${this.variantAnnotation.chromosome}:${this.variantAnnotation.start}:${this.variantAnnotation.reference}:${this.variantAnnotation.alternate}`;

Expand Down
20 changes: 10 additions & 10 deletions src/webcomponents/variant/interpretation/variant-interpreter-browser-cancer.js
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Expand Up @@ -530,17 +530,17 @@ class VariantInterpreterBrowserCancer extends LitElement {
],
result: {
grid: {
pagination: true,
pageSize: 10,
pageList: [5, 10, 25],
showExport: false,
detailView: true,
showReview: false,
showActions: true,
// pagination: true,
// pageSize: 10,
// pageList: [5, 10, 25],
// showExport: false,
// detailView: true,
// showReview: false,
// showActions: true,
showSelectCheckbox: true,
multiSelection: false,
nucleotideGenotype: true,
alleleStringLengthMax: 10,
// multiSelection: false,
// nucleotideGenotype: true,
// alleleStringLengthMax: 10,

genotype: {
type: "VAF"
Expand Down
20 changes: 10 additions & 10 deletions src/webcomponents/variant/interpretation/variant-interpreter-browser-cnv.js
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Expand Up @@ -413,17 +413,17 @@ class VariantInterpreterBrowserCNV extends LitElement {
],
result: {
grid: {
pagination: true,
pageSize: 10,
pageList: [5, 10, 25],
showExport: false,
detailView: true,
showReview: false,
showActions: true,
// pagination: true,
// pageSize: 10,
// pageList: [5, 10, 25],
// showExport: false,
// detailView: true,
// showReview: false,
// showActions: true,
showSelectCheckbox: true,
multiSelection: false,
nucleotideGenotype: true,
alleleStringLengthMax: 10,
// multiSelection: false,
// nucleotideGenotype: true,
// alleleStringLengthMax: 10,

hideType: true,
hidePopulationFrequencies: true,
Expand Down
20 changes: 10 additions & 10 deletions src/webcomponents/variant/interpretation/variant-interpreter-browser-rd.js
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Expand Up @@ -545,17 +545,17 @@ class VariantInterpreterBrowserRd extends LitElement {
],
result: {
grid: {
pagination: true,
pageSize: 10,
pageList: [5, 10, 25],
showExport: false,
detailView: true,
showReview: true,
showActions: true,
// pagination: true,
// pageSize: 10,
// pageList: [5, 10, 25],
// showExport: false,
// detailView: true,
// showReview: true,
// showActions: true,
showSelectCheckbox: true,
multiSelection: false,
nucleotideGenotype: true,
alleleStringLengthMax: 10,
// multiSelection: false,
// nucleotideGenotype: true,
// alleleStringLengthMax: 10,

header: {
horizontalAlign: "center",
Expand Down
18 changes: 9 additions & 9 deletions src/webcomponents/variant/interpretation/variant-interpreter-browser-rearrangement.js
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Expand Up @@ -418,16 +418,16 @@ class VariantInterpreterBrowserRearrangement extends LitElement {
],
result: {
grid: {
pagination: true,
pageSize: 10,
pageList: [5, 10, 25],
showExport: true,
detailView: true,
showReview: false,
showActions: true,
// pagination: true,
// pageSize: 10,
// pageList: [5, 10, 25],
// showExport: true,
// detailView: true,
// showReview: false,
// showActions: true,
showSelectCheckbox: true,
multiSelection: false,
nucleotideGenotype: true,
// multiSelection: false,
// nucleotideGenotype: true,
alleleStringLengthMax: 25,
header: {
horizontalAlign: "center",
Expand Down
18 changes: 13 additions & 5 deletions src/webcomponents/variant/interpretation/variant-interpreter-grid.js
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Expand Up @@ -164,12 +164,12 @@ export default class VariantInterpreterGrid extends LitElement {
this.gridCommons = new GridCommons(this.gridId, this, this._config);

this.toolbarSetting = {
showCreate: false,
showExport: true,
showSettings: true,
exportTabs: ["download", "export", "link", "code"], // this is customisable in external settings in `table.toolbar`
// ...this._config,
// it comes from external settings
showColumns: false,
showSettings: true,
...this._config,
// columns: defaultColumns[0].filter(col => col.rowspan === 2 && col.colspan === 1 && col.visible !== false),
// gridColumns: defaultColumns, // original column structure
Expand All @@ -178,6 +178,7 @@ export default class VariantInterpreterGrid extends LitElement {
this.toolbarConfig = {
toolId: this.toolId,
resource: "CLINICAL_VARIANT",
disableCreate: true,
showInterpreterConfig: true,
columns: this._getDefaultColumns()
};
Expand Down Expand Up @@ -409,7 +410,7 @@ export default class VariantInterpreterGrid extends LitElement {
formatShowingRows: this.gridCommons.formatShowingRows,
showExport: this._config.showExport,
detailView: this._config.detailView,
detailFormatter: (value, row) => this.detailFormatter(value, row),
detailFormatter: this._config.detailFormatter,
formatLoadingMessage: () => "<div><loading-spinner></loading-spinner></div>",

// this makes the opencga-interpreted-variant-grid properties available in the bootstrap-table formatters
Expand Down Expand Up @@ -1532,13 +1533,20 @@ export default class VariantInterpreterGrid extends LitElement {

getDefaultConfig() {
return {
// Bootstrap Grid config
pagination: true,
pageSize: 10,
pageList: [5, 10, 25],
showExport: false,
detailView: true,
showReview: true,
detailFormatter: this.detailFormatter,
// multiSelection: false,

// Custom config
showToolbar: true,
showCreate: false,
showExport: true,
showSettings: true,
showReview: true,
showSelectCheckbox: false,
showActions: true,
showEditReview: true,
Expand Down
12 changes: 10 additions & 2 deletions src/webcomponents/variant/variant-browser-grid.js
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Expand Up @@ -139,11 +139,14 @@ export default class VariantBrowserGrid extends LitElement {
...this.getDefaultConfig(),
...this.config,
};

this.gridCommons = new GridCommons(this.gridId, this, this._config);

// Config for the grid toolbar
this.toolbarSetting = {
showCreate: false,
showExport: true,
showSettings: true,
exportTabs: ["download", "export", "link", "code"], // this is customisable in external settings in `table.toolbar`
showColumns: false,
...this._config,
Expand Down Expand Up @@ -1064,16 +1067,21 @@ export default class VariantBrowserGrid extends LitElement {

getDefaultConfig() {
return {
// Bootstrap Grid config
pagination: true,
pageSize: 10,
pageList: [5, 10, 25],
showExport: false,
detailView: true,
detailFormatter: this.detailFormatter,
// multiSelection: false,

// Custom config
showToolbar: true,
showCreate: false,
showExport: true,
showSettings: true,
showSelectCheckbox: false,
showActions: true,
multiSelection: false,
nucleotideGenotype: true,
alleleStringLengthMax: 15,

Expand Down
13 changes: 8 additions & 5 deletions src/webcomponents/variant/variant-browser.js
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Expand Up @@ -673,7 +673,7 @@ export default class VariantBrowser extends LitElement {
name: "Consequence Type",
render: (variant, active) => html`
<variant-consequence-type-view
.consequenceTypes="${variant.annotation.consequenceTypes}"
.consequenceTypes="${variant?.annotation?.consequenceTypes}"
.active="${active}">
</variant-consequence-type-view>
`,
Expand All @@ -683,7 +683,7 @@ export default class VariantBrowser extends LitElement {
name: "Population Frequencies",
render: (variant, active) => html`
<cellbase-population-frequency-grid
.populationFrequencies="${variant.annotation.populationFrequencies}"
.populationFrequencies="${variant?.annotation?.populationFrequencies}"
.active="${active}">
</cellbase-population-frequency-grid>
`,
Expand All @@ -693,8 +693,8 @@ export default class VariantBrowser extends LitElement {
name: "Clinical",
render: variant => html`
<variant-annotation-clinical-view
.traitAssociation="${variant.annotation.traitAssociation}"
.geneTraitAssociation="${variant.annotation.geneTraitAssociation}">
.traitAssociation="${variant?.annotation?.traitAssociation}"
.geneTraitAssociation="${variant?.annotation?.geneTraitAssociation}">
</variant-annotation-clinical-view>
`,
},
Expand Down Expand Up @@ -737,7 +737,10 @@ export default class VariantBrowser extends LitElement {
id: "json-view",
name: "JSON Data",
render: (variant, active) => html`
<json-viewer .data="${variant}" .active="${active}"></json-viewer>
<json-viewer
.data="${variant}"
.active="${active}">
</json-viewer>
`,
}
// TODO Think about Neeworks
Expand Down
2 changes: 1 addition & 1 deletion src/webcomponents/variant/variant-utils.js
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Expand Up @@ -69,7 +69,7 @@ export default class VariantUtils {
"gene",
"type",
// Adding SAMPLES (includeSample=all in VB and Case samples in Sample VB)
...samples.map(sample => sample.id),
...samples.map(sample => sample.id || sample),
"consequenceType",
"deleteriousness.SIFT",
"deleteriousness.polyphen",
Expand Down
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