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Customizable Dynamic Kaplan-Meier Plot for Survival Analysis #4900

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Customizable Dynamic Kaplan-Meier Plot for Survival Analysis #4900

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4f50e27
Resolve fetching genomic chart datatype for logged in user
kalletlak Sep 22, 2023
63f973e
Add dynamic survival plot
kalletlak Sep 27, 2023
6847ea3
Merge branch 'master' into fix-10375
qlu-cls Mar 21, 2024
135f160
support censored events dropdown
qlu-cls Mar 28, 2024
50bdfff
survival table and plot visibility
qlu-cls Apr 2, 2024
0bd705a
open all clinical event types and add any type
qlu-cls Apr 16, 2024
42739b3
support configurable clinical events
qlu-cls Apr 17, 2024
308dd66
update custom survival plot data to LocalStorage
qlu-cls May 2, 2024
28486ed
Merge remote-tracking branch 'upstream/master' into fix-10375
qlu-cls May 14, 2024
727f897
Merge branch 'master' into fix-10375
7xuanlu May 14, 2024
ca3c51d
create new session for updated custom survival plots
qlu-cls May 17, 2024
82dca0b
fix delete chart return null page
qlu-cls Jun 19, 2024
add49f4
Merge branch 'master' into fix-10375
kalletlak Jul 8, 2024
e99fda0
Update jitpack-build.yml
kalletlak Jul 8, 2024
7e395ed
Tweaks
kalletlak Sep 20, 2024
f0598a7
Revert back Jitpack
kalletlak Sep 20, 2024
0520f68
Move KM plot creation to modal
kalletlak Sep 27, 2024
199fec7
Fix issues running UI
kalletlak Sep 27, 2024
2d7ea7a
Only Add survival plot when there is clinical event data
kalletlak Sep 27, 2024
d7fcfb3
Cleanup
kalletlak Sep 27, 2024
c58b8e7
Updates to plot name and description
kalletlak Oct 1, 2024
1854a2f
Fix chart name dulipcation bug
kalletlak Oct 2, 2024
df1a285
Update notification and descriptions
kalletlak Oct 8, 2024
f442cc4
Merge remote-tracking branch 'cbio/master' into fix-10375
kalletlak Oct 8, 2024
996fda1
Fix issue with duplicate plot name
kalletlak Oct 8, 2024
1c5073e
Refactor comparison store
kalletlak Oct 12, 2024
1930cd6
Cleanup
kalletlak Oct 15, 2024
c2eaf0f
Show add button when only clinical event data present
kalletlak Oct 16, 2024
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3 changes: 2 additions & 1 deletion end-to-end-test/remote/specs/core/comparisonTab.screenshot.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -422,7 +422,8 @@ describe('results view comparison tab screenshot tests', () => {
await waitForElementDisplayed('b=RER1', { timeout: 10000 });
await clickElement('b=RER1');
await (await getElement('body')).moveTo({
x:0, y:0
x: 0,
y: 0,
});
const res = await browser.checkElement(
'.msk-tab:not(.hiddenByPosition)',
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2 changes: 1 addition & 1 deletion env/master.sh
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
export CBIOPORTAL_URL="${CBIOPORTAL_URL:-https://www.cbioportal.org}"
export CBIOPORTAL_URL="${CBIOPORTAL_URL:-https://master.cbioportal.org}"
export GENOME_NEXUS_URL="${GENOME_NEXUS_URL:-https://www.genomenexus.org}"
export BACKEND=cbioportal:demo-fix-clinical-table-sorting
319 changes: 319 additions & 0 deletions package-lock.json
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we shouldn't need package lock. use yarn to add new things, not npm

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4 changes: 2 additions & 2 deletions package.json
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Expand Up @@ -82,7 +82,6 @@
"author": "",
"license": "AGPL-3.0-or-later",
"dependencies": {
"3dmol": "^1.3.7",
"@babel/core": "7.4.4",
"@babel/plugin-syntax-dynamic-import": "^7.8.3",
"@babel/plugin-transform-modules-commonjs": "^7.4.4",
Expand Down Expand Up @@ -145,6 +144,7 @@
"@types/seedrandom": "2.4.27",
"@types/sinon": "^4.1.3",
"@types/superagent": "^2.0.36",
"3dmol": "^1.3.7",
"addthis-snippet": "^1.0.1",
"autobind-decorator": "^2.1.0",
"autoprefixer": "^6.7.0",
Expand Down Expand Up @@ -195,7 +195,6 @@
"html-webpack-plugin": "^5.3.2",
"igv": "^2.11.2",
"imports-loader": "^0.8.0",
"jStat": "^1.7.0",
"javascript-natural-sort": "^0.7.1",
"jquery": "3.6.0",
"jquery-migrate": "3.0.0",
Expand All @@ -204,6 +203,7 @@
"json-fn": "^1.1.1",
"jsonpath": "^1.1.1",
"jspdf": "^1.3.3",
"jStat": "^1.7.0",
"jstree": "^3.3.4",
"jszip": "^3.7.1",
"lerna": "3.19.0",
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3 changes: 3 additions & 0 deletions packages/cbioportal-ts-api-client/src/index.tsx
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Expand Up @@ -77,6 +77,9 @@ export {
StructuralVariantFilter,
StructuralVariantQuery,
StructuralVariantGeneSubQuery,
ClinicalEventRequest,
ClinicalEventRequestIdentifier,
SurvivalRequest,
StructuralVariantFilterQuery,
GeneFilterQuery,
AndedSampleTreatmentFilters,
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1 change: 1 addition & 0 deletions src/config/IAppConfig.ts
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Expand Up @@ -172,6 +172,7 @@ export interface IServerConfig {
skin_comparison_view_mutation_table_columns_show_on_init: string;
skin_patient_view_copy_number_table_columns_show_on_init: string;
skin_patient_view_structural_variant_table_columns_show_on_init: string;
skin_survival_plot_clinical_event_types_show_on_init: string;
skin_results_view_tables_default_sort_column: string;
skin_patient_view_tables_default_sort_column: string;
skin_patient_view_custom_sample_type_colors_json: string;
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2 changes: 2 additions & 0 deletions src/config/serverConfigDefaults.ts
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Expand Up @@ -224,6 +224,8 @@ export const ServerConfigDefaults: Partial<IServerConfig> = {

skin_patient_view_structural_variant_table_columns_show_on_init: '',

skin_survival_plot_clinical_event_types_show_on_init: '',

skin_results_view_tables_default_sort_column: 'Annotation',

skin_patient_view_tables_default_sort_column: 'Annotation',
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