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Add a new survival data api endpoint that supports customizable Dynamic Kaplan-Meier plot. --------- Co-authored-by: Karthik <[email protected]> Co-authored-by: Qi-Xuan Lu <[email protected]>
Remove demo-rfc72 reference from integration test
Frontend v6.0.9
…n their landing pages (#10829) * Implement endpoints for public virtual studies * Add possibility to specify cancer type id and pmi for virt. study during publishing * Filter out forbidden study ids from virtual studies * Do not allow set * user for user virtual study To prevent missuse of the request to publish virtual study for everyone! * Add integration tests for (un)publishing virtual study * Assert fields fo published virtual studies * Use recommended ways to inject dependencies in spring * Add issue link to session service FIXMEs * Fix sonar reported NPE bugs * Remove unnecessary checks for null * Remove obsolete TODO comment * Throw AccessForbiddenException and use GlobalExceptionHadler instead * Throw IllegalStateException is downstream server return unsuccessful result * Remove raw use of ResponseEntity * Throw bad request exception instead of returning ResponseEntity * Do not filter out VS when user does not hava access to underlying study samples * Fix integration tests * Extract http calls to the session service to the handler * Remove todo comment User has to have * username witch is not likely * Fix sonarcloud issues * Deduplicate ensuring publisher api key is correct * Remove usage of generic wildcard type * Extract logic to update VS metadata fields into a method * Document publishing virtual study feature * Update docs/Create-And-Publish-Virtual-Study.md Co-authored-by: pieterlukasse <[email protected]> * Publish virtual study by modifying it instead of making copy Also get rid of undocumented endpoint * Improve name and docs of method to retrieve VS for user * Assign VM after un-publshing to the owner Make sure that we unpublish public virtual study. Fail otherwise. --------- Co-authored-by: Charles Haynes <[email protected]> Co-authored-by: pieterlukasse <[email protected]>
* restrict proxy access to known hosts only * remove proxy/** endpoint
* Add Incremental Data Loading Documentation * Apply suggestions from code review Co-authored-by: pieterlukasse <[email protected]> --------- Co-authored-by: pieterlukasse <[email protected]>
For publishing and un-publishing we use token base authorisation
* fix: allow empty genepanel query for API requests on study without gene panel data --------- Co-authored-by: Aiosa <[email protected]> Co-authored-by: Ino de Bruijn <[email protected]>
* update cache action
* support custom springboot args for api-tests * fix typo
* Add all usecases for studyview service * Fix apiTests * 📝 Add docs for new clickhouse classes * add ability to extract study ids without involvedCancerStudy interceptor * Move to domain module * Extract UseCases * Move tests for domain specific Repositories * Make sonar fixes * Remove docs
* Test v6.0.27 * Test uppercase groupId
* Remove servlet-api dependency from mockserver-client-java * Update documentation to reflect the change of removing servlet-api package
* Fixes to standalon documentation
* Fix frequency issue for same genePanel Rebase to original branch
…pose (#11433) * add documentation for clickhouse mode setup for cbioportal docker compose * update clickhouse compatible release * improve study import docs
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