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* SnpEff integration prototyping * Semi-functional prototype snpEff interface * SnpEff prototype — annotation successful * Reorganization * Switch to a serious implementation * Add an interface for SnpEff annotation * Fix annotation config and interface * Add proper SnpEff configuration * Beqin SnpEff database management * Start snpEff database download * Add automatic genome download * Add snpEff genome installation * Add online building of SnpEff database * Minor change * fix: default genome download seems ok but 1sec download genome can crash * fix: snpeff upload from files seems ok * fix: snpeff import ok + start seems ok * Improvements on SnpEff integration * Minor fix * Split up shared code from main.js into common.js (#131) * 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 * Worked around filtering by IDs disabling variant type filter This is causing issues for exporting into formats that don't support all variant types * Reverted accidental commit * Provided means to rearrange metadata columns' order * Merge from master (#150) * 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> * Corrected css file contents * Provided means to set DB taxonomy thru back-office * Fixed bug in switching from species to another level * Minor fix * Merged Staging & Custom look (#155) * Added means to customize look * Merge from master (#114) * Moved standalone IGV download link to "Online output tools" dialog * added OAuth token compatibility for API requests, based on an OIDC discovery file (#112) Co-authored-by: GuilhemSempere <guilhem.sempere@cirad.fr> * Revert "added OAuth token compatibility for API requests, based on an OIDC discovery file (#112)" This reverts commit a899c7f. --------- Co-authored-by: Peter Selby <32845555+BrapiCoordinatorSelby@users.noreply.github.com> * Merge from master (#119) * Moved standalone IGV download link to "Online output tools" dialog * added OAuth token compatibility for API requests, based on an OIDC discovery file (#112) Co-authored-by: GuilhemSempere <guilhem.sempere@cirad.fr> * Revert "added OAuth token compatibility for API requests, based on an OIDC discovery file (#112)" This reverts commit a899c7f. * Caching unzoomed results for fast zoom resets ... also reduced dot size and set default number of intervals to 1000 * Fixed dialog height (set to maximum for all) --------- Co-authored-by: Peter Selby <32845555+BrapiCoordinatorSelby@users.noreply.github.com> --------- Co-authored-by: Peter Selby <32845555+BrapiCoordinatorSelby@users.noreply.github.com> * Revert "Merged Staging & Custom look (#155)" This reverts commit 9845774. * override listReadablesDb * Fixed position range paste issue (stripping out non-digits) * POM version update * Fixed minor UI issue * Custom look (#156) * Provided means to customize the UI (Windows update script not tested yet) * Fixed Windows update script * Fixed export file cleanup rate * Fixed missing header in IGV data table when no markers in displayed area * Fixed scrollbar bugs, optimized initial genotype loading, ... * Minor UI fix * Handle uploaded files while HTTP request is valid * Minor UI fix * Accounted for newly added role, allowing to create DBs * Removed forbidMongoDiskUse config parameter * Moved VisualizationService class from Gigwa2ServiceImpl to Mgdb2Export * Minor UI fix * Minor UI improvements * Minor UI improvements * Fixed startup bug occurring when no trait data available * Minor change * Sorted out dodgy import UI behaviour when typing an existing DB's name * Only check authorities if not anonymous * Documentation update for v2.9 * Added screenshot to documentation * Update README.md (#158) (#159) * Skipping Unit Tests whein building staging vesion * Persist skip-monomorphic-variant-import-box state into localStorage * Made it possible to push to Galaxy even when running on localhost * Changed version * Re-commitiing omitted file * Keeping vcf.gz compressed on Galaxy side when not running on localhost * Merge from master (#161) * Update README.md (#158) * Update genomes.json add Leccino genome (#160) --------- Co-authored-by: droc <gaetan.droc@cirad.fr> * Making UI able to work with samples instead of individuals * Removed accidentally added parameters * Moving towards making UI & exports support working with samples * Fixed 2 small startup bugs * Made VizService compatible with detached samples * Made IGV data export compatible with detached samples * Minor fix * Only showing "Work on samples" checkbox when appropriate * Persisted workWithSamples status in localStorage * Made password reset work without using the HttpSession * Minor change * Import refactoring and Split Sample into 2 new collections : IndSample and CallSets * Remove pj and rn fields from GenotypingSample and update queries to get callsets from individuals * Add workWithSample param in getQuery, and bookmark * Add missing update from previous commit * Implementing multi-project UI + addition of callset entity * Further integrating multi-projet UI + callSet level addition * Fixed some issues in displaying genotypes by individual or sample * Minor fix * Made BrAPI v1 import compatible with Gigwa CallSets * Minor fix * Minor change * Update Terminology correspondence table for APIs * Minor fix * CallSets now embedded in Samples * Fixing errors due to addition of CallSet level * add config parameters for allelematrixSearch limit pageSize * Ready for testing * Minor changes * Removed unused parameter * Minor changes * Fixed chart sequence list * fix getting metadata from several projects * fix tests error when cleaning after testing * fix call distinctSampleMetadata with list of projects * Fixed remaining issues in handling multiple project IDs * Sort genotype table by individual, then project, then run * Implemented fix for accidentally published "internal" config properties * Corrected "internal" trackerUrl value * Minor fix * Added a 5 sec timeout to the attempts of listing DB dump files * Minor change * Set a limit (10) to number of simultaneously displayed metadata fields * Save workWithSample in localStorage depending on DB * Show also individuals metadata when loading samples metadata * Minor change * Minor change * Account for metadate field value selection only when closing dropdown * Implemented example MD file download, supporting mandatory fields * Minor change * Mentioning mandatory fields in example metadata files (+ minor fix) * Added support for ignoring comment lines in metadata files * Minor fixes * new: mandatoryIndividualMetadata-DB_NAME mandatorySampleMetadata-DB_NAME * Now supporting global (not only per-DB) mandatory metadata fields * Minor change * Updated documentation to match v2.10 features * Minor change * Fixed filter object structure for sample's individual metadata in graphs * Minor change * Added support for description for mandatory metadata fields * Updated documentation to mention mandataory metadata fields * Minor change * Minor change * Sped up metadata distinct values loading when used as Fst groups * Updated new param description & example values * Minor fixes * Provided means to ask for confirmation before switching module to public Also made dirtiness handling more clever * Added termsToAcceptToMakeDatabasePublic config parameter * For mandatory metadata fields prefixed with *, require non-blank values * Reduced project info box z-index * Reworked Terms Of Use dialog display - cookie duration now configurable - cookie expiration is no more pushed back while the system is being used (delay counting now strictly starts when the agreement button is clicked) - dialog can be displayed explicitly via a link on the homepage - dialog contents can be customized by appending HTML defined via a config property * Updated version number * Fixed minor UI bug * Updated config.properties * Removed useless dependency * Minor fix * Minor change * Minor changes in chart UI to be compatible with WIDDE * IntertekImport - map alleleX and alleleY on knownAlleles if variant exist in database. * Integrated smart-color-multiselect for Fst group selection * Fixed issues handling groups for charts * Added heterozygosity chart support * Minor changes * Minor change * Now using newly created ExportHelper class to provide tool URLs * Update dependencies and Tomcat version in pom.xml * Merge branch 'staging' of https://github.com/SouthGreenPlatform/Gigwa2.git into snpEff * Minor fix * Minor changes * Version update * Added UI in admin to fix VRD records with missing known alleles * Added missing data graph * Changed ref allele bgcolor in variant details popup * Minor change * Minor documentation change * Fix importing metadata on samples * updated MANIFEST * Refactored numbering of items in Terms Of Use box * Update genomes.json (#173) (#174) Co-authored-by: droc <gaetan.droc@cirad.fr> * Removed commented-out code * Fixed issue in grouping bio-entities by color for Fst graph * Added means to increase the graph width * Manage cookie consent properly via checkbox * Fixed minor issues * POM update * Version update * Reintroduced lost change (fix for supporting metadata fields with trailing spaces) --------- Co-authored-by: Grégori Mignerot <gregori.mignerot@cirad.fr> Co-authored-by: Yoan BIGGIO <yoan.biggio@epita.fr> 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> Co-authored-by: Peter Selby <32845555+BrapiCoordinatorSelby@users.noreply.github.com>
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