[bot] Merge 26.7 to develop#661
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#### Changes **Test actions globally swap the NcbiPublicationSearchService singleton with no audit event (Informational)** * The three Selenium-test support actions (`SetupMockNcbiServiceAction`, `RestoreNcbiServiceAction`, `RegisterMockPublicationAction`) swap a process-wide singleton. They are @RequiresSiteAdmin but otherwise reachable in production, and extended ReadOnlyApiAction, which does no CSRF check and is reachable by a plain GET. * Added `requireDevModeForMockNcbiService()`: the actions now return 404 on a non-dev-mode server. Dev machines and TeamCity run in dev mode, so tests are unaffected. * Changed the three actions from `ReadOnlyApiAction` to `MutatingApiAction`, since they mutate global state, which also requires a POST with a CSRF token. * The report suggested adding an audit event or compiling these out of production builds. On review we found that gating them to dev mode is a better fix, since it removes the production attack surface entirely rather than just recording the swap. **Uses System.out instead of Log4J2 (Informational)** * `ExperimentModificationGetter`: removed System.out helpers printStructuralMod and printIsotopicMod and their call sites. **Tests** * `PublicationSearchTest`: invoke the three mock-NCBI actions with `SimplePostCommand `instead of `SimpleGetCommand`.
#### Changes ***Stored XSS (High) - result views and email preview** * failureDetail.jsp: HTML-encode the failure language and stack trace * runDetail.jsp: render the run log/xml popup via a `<pre>` textContent node instead of document.write of concatenated HTML. * trainingdata.jsp: render the daily-email preview in a sandboxed iframe (scripts disabled, opaque origin) instead of document.write of the raw email HTML. **Transaction and SQL handling (Medium)** * ChangeBoundaries.execute: wrapped the GlobalSettings update transaction in try-with-resources so it cannot leak on an exception before commit, and parameterized the INSERT with bind parameters. **Daily email output encoding (Low)** * SendTestResultsEmail.getHTMLEmail: HTML-encode the git hash, missing-user name, problem-table computer name, and test name. **Logging hygiene (Low)** * Replaced all five e.printStackTrace() calls with Log4J2 logging that includes the exception. **Tests** * Added testViewLogPopup, which opens the run-log popup and asserts the stored log is displayed (the existing tests only exercised the ViewLog API).
cnathe
approved these changes
Jul 8, 2026
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Merging changes from: bf07c79
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