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RFC83: Make virtual study available for all users on their landing pages #4923

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merged 7 commits into from
Jul 18, 2024

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@forus forus commented Jun 13, 2024

Fix cBioPortal/cbioportal# (see https://help.github.com/en/articles/closing-issues-using-keywords)

Describe changes proposed in this pull request:

  • Introduce an admin call, secured by a secret key, to publish virtual studies for all users, making them visible on the landing page.

Backend cBioPortal/cbioportal#10829

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  • Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
  • The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
  • Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

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forus commented Jun 21, 2024

@alisman Hi! Could you please provide some guidance on which tests I should write for this PR?

@forus forus changed the title RFC83: Add admin call to make virtual study available for all users on their landing pages RFC83: Make virtual study available for all users on their landing pages Jul 4, 2024
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Looks good to me. Only a few minor questions.

I understand tests will still be added. I can also review those once available 👍

@@ -17,6 +17,14 @@ export default class sessionServiceAPI {
return `${getSessionUrl()}/virtual_study`;
}

getPublicVirtualStudyServiceUrl() {
//FIXME change url after moving the code to the session controller
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are we fixing this?

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Yes, here it is 2aea3c5

//map public virtual study to cancer study
const _publicVirtualStudies = publicVirtualStudies
.map(publicVirtualStudy => {
// TODO: temp fix for when virtual study data is not of expeceted format
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will this be added or is it a separate ticket?

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nea, let's just clean it. 2ac225d

@@ -14,6 +14,7 @@ import { FilteredCancerTreeView } from '../StudyListLogic';
import {
CancerTreeNode,
CancerTypeWithVisibility,
PUBLIC_VIRTUAL_STUDY_NAME,
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not used?

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indeed, 6528be0

@alisman alisman merged commit 9ca3198 into master Jul 18, 2024
14 of 15 checks passed
@alisman alisman deleted the rfc83 branch July 18, 2024 20:24
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3 participants