[bot] Merge 25.11 to 26.3 (Conflicts)#618
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github-actions[bot] merged 4 commits intorelease26.3-SNAPSHOTfrom Mar 24, 2026
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[bot] Merge 25.11 to 26.3 (Conflicts)#618github-actions[bot] merged 4 commits intorelease26.3-SNAPSHOTfrom
github-actions[bot] merged 4 commits intorelease26.3-SNAPSHOTfrom
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- Added a setting in the admin console (Private Data Reminder Settings) to enable publication search - Added NcbiPublicationSearchService that searches for publications in -- PubMed Central (full-text available): search terms ProteomeXchange Id, Panorama Public short URL, Panorama Public DOI. Author and title verified. -- PubMed - fallback if no matches found in PMC; search author and title only since PubMed does not have full-text articles -- Preprints (e.g. biorxiv, medrxiv etc.) are filtered out -- Results are prioritized by number of matched search terms (e.g. PX ID, Panorama link) as well as paper publication date proximity to data submission date - Publication search happens automatically in the PrivateDataReminderJob when enabled in the admin console - Publications for a single dataset can also be searched through the Search Publications menu item in the _TargetedMS Experiment_ webpart menu - If a publication match is found during the PrivateDataReminderJob, instead of the usual reminder message, a "publication found" message is posted to the submitter - Submitter can dismiss suggested publication by clicking the Dismiss Publication Suggestion link in the message. - DatasetStatus caches publication result to avoid repeated calls to NCBI's EUtils endpoints - Moved NCBI citation lookup methods to NcbiPublicationSearchServiceImpl - **Tests** -- Unit tests added in NcbiPublicationSearchServiceImpl -- Added Selenium test PublicationSearchTest -- Test uses a mock NCBI service on TeamCity (mocking only the outbound HTTP requests) so all real search and filtering logic is exercised without live API calls.
* Added documentation support to Skyline Tool Store * Extract docs from tool-inf/docs/ in uploaded ZIPs and serve via WebDAV * Carry forward docs from previous version when new ZIP has none * Show "Online Documentation" link in Documentation box when docs exist * Skip tool-inf/docs/ images during icon extraction * Exclude docs dir from supplementary file listings * Fall back to /home/support when no tool-specific support board exists Co-Authored-By: Claude <noreply@anthropic.com> * Hide "Support Board" button when no target container can be resolved Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Avoid calling tool.hasDocumentation() twice Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * Change condition to use toolIcon == null to avoid scanning the entire tool ZIP Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> * - Fixed getDocsUrl() to use WebdavService.getPath() instead of hardcoded /_webdav string - Fixed hasDocumentation() to use Files.exists() instead of new File().exists() - getLocalPath() returns Path directly instead of converting to File - Updated getSupplementaryFileBasenames() to use Files.list() instead of File.list() - Refactored extractDocsFromZip() to use NIO Path - Use FileUtil.copyDirectory(Path, Path) to copy docs from previous tool version * Added visually-hidden tool name to download buttons for accessibility * Screen readers can now distinguish download buttons by tool name Co-Authored-By: Claude <noreply@anthropic.com>
* Added accessibility and docs support to tool listing page * Added visually-hidden tool name to Download and Documentation buttons * Show Documentation button when tool has docs extracted from ZIP * - Replaced <a><button> nesting with link() builder - Added display:inline-flex; and align-items:center; to styled-button CSS class for consistent appearance with <button> * Converted Download <button> to <a> using link() builder for consistency * Added a.styled-button CSS for text-decoration and visited color * Moved space into visually-hidden span as to prevent collapsing Co-Authored-By: Claude <noreply@anthropic.com>
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