Merge from master #137
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Merge from master #137
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Merge from staging
Final adjustments before release, documentation update
Update build.yml
GuilhemSempere
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Oct 2, 2024
* Update pom.xml * Create MIT.txt (#130) * Update LICENSE.txt * Create AGPL-3.0.txt * Removed useless files * Revert "added OAuth token compatibility for API requests, based on an OIDC discovery file (#113)" * Split up shared code from main.js into common.js * Set version number to 2.8-RELEASE * Final adjustments before release, documentation update * Added missing file (possibly forgot to commmit/push it) * Merge from master (#137) * Update build.yml * Reverted back to original build.sh * Added missing file (possibly forgot to commmit/push it) (#136) * Re-added lost methods * Embed Oracle JDK instead of Zulu JRE into bundles * Now averaging cumulated VCF field values on #variants per interval * Finalized calculation of VCF numeric field series as averaged ... rather than cumulated, as it used to be. * Fixed VCF field series removal ... also set MongoDB password via placeholder in applicationContext-data.xml, to avoiding pushing passwords to source control * Merge from master (#139) * Update build.yml * Reverted back to original build.sh * Added missing file (possibly forgot to commmit/push it) (#136) * added python build file to get dynamically current pom.xml dependencies, add build.sh deprecated and improve current github workflow (#138) Co-authored-by: Dorian Grasset <dorian.grasset@cirad.fr> --------- Co-authored-by: Dorian Grasset <dorian.grasset@cirad.fr> * Added support for user email addresses * Displaying imports in admin process list (#140) * feat(execution-message): update GigwaModuleManager * Finalized inclusion of import processes in admin-process list * Finalized display of imports in admin process list --------- Co-authored-by: Dorian Grasset <dorian.grasset.contact@gmail.com> * Feat/change password (#141) * feat(change-password): added a menu for logged in users to change password * feat(change-password): send mail code * feat(change-password): add new services * feat(change-password): feature implemented * feat(change-password): handle password > 20 characters error and update email message * feat(change-password): put reset code logic in session * feat(change-password): add enforcedWebapRootUrl var * Sorted out a few details on password override functionality --------- Co-authored-by: Dorian Grasset <dorian.grasset.contact@gmail.com> * Merged password recovery feature * Fixed default JavaMailSenderImpl config: no credentials if auth disabled * Made dumpFolder checking more robust (10sec timeout) * Minor fixes / changes * Suggest user to enter an e-mail address if reset functionality is active * POM.xml version update * Added HTML version to password reset e-mail (+ skipped for SSO users) * Better handle security exceptions * Simplified XML context file loading + enabled global-method-security * Update build-staging.yml * Added forgotten class * Made online output tools available for async-watched exports * Fixed login issue (redirection to administration was remaining active) * Minor fix * add function to check if the user can edit calls and display snpclust button also for reader role * Fixed import process cleanup * Merge from master (#145) * Update build.yml * Reverted back to original build.sh * Added missing file (possibly forgot to commmit/push it) (#136) * added python build file to get dynamically current pom.xml dependencies, add build.sh deprecated and improve current github workflow (#138) Co-authored-by: Dorian Grasset <dorian.grasset@cirad.fr> * Update genomes.json Add 4 new genomes for Citrus medica, C. micrantha, C. maxima and C. reticulata --------- Co-authored-by: Dorian Grasset <dorian.grasset@cirad.fr> Co-authored-by: droc <gaetan.droc@cirad.fr> * Export optim (#146) * DDL is now fake (deleting file after 1 hour) This is a counterpart for removing the need for very long timeout settings * Made IGV data retrieval compatible with multithreaded export * Parallelized export functional IGV display * Minor change * IGV export is now handled via HapmapExportHandler * Minor changes * Made export file cleanup happen periodically * Minor changes * Minor change * Fixed slight interface issues * Enabled AutoUnzipFilter for DDL exports * Enhanced export flexibility regarding ability to push to external tools * Changed project version * Dynamically accounting for changes in custom output tool configuration * Minor UI fix * Minor UI changes * Fixed bug in reloading saved trait settings --------- Co-authored-by: Dorian Grasset <dorian.grasset@cirad.fr> Co-authored-by: Dorian Grasset <dorian.grasset.contact@gmail.com> Co-authored-by: Alice Boizet <alice.boizet@cirad.fr> Co-authored-by: droc <gaetan.droc@cirad.fr>
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