Releases: GuilhemSempere/Mgdb2
Releases · GuilhemSempere/Mgdb2
Release list
2.13-RELEASE
POM update
2.12-RELEASE: Staging (#96)
* Prepared for annotation system support * Removed accidentally added dependency * Account for multiple variant types in findDefaultRangeMinMax * Fixed issue in bio-entity ordering when exporting DARwin .don file * Fix allele lists in previous VRD records when encountering new alleles * Made ExpiringHashMap support sliding TTL * Staging (#94) (#95) * Prepared for annotation system support * Removed accidentally added dependency * Account for multiple variant types in findDefaultRangeMinMax * Fixed issue in bio-entity ordering when exporting DARwin .don file * Fix allele lists in previous VRD records when encountering new alleles * Made ExpiringHashMap support sliding TTL * Minor change * POM update
2.11-RELEASE: Staging (#93)
* Prepared for annotation system support * Removed accidentally added dependency * Account for multiple variant types in findDefaultRangeMinMax * Fixed issue in bio-entity ordering when exporting DARwin .don file * Fix allele lists in previous VRD records when encountering new alleles
2.10-RELEASE
Merge branch 'staging' of https://github.com/GuilhemSempere/Mgdb2.git
2.9-RELEASE: Merged from staging for next release (#80)
* Added means to import INDELs from PLINK data, alleles encoded as I and D ... the workaround to make it htsjdk compatible is turning I into NN and D in to N * Generalizing support for I and D alleles * add function to check if the user can edit calls * Exporting alleles of INDELs with unknown sequence as I/D for all individual-oriented formats * Export optim (#78) * Implemented async exports from temp collections * POM dependency upgrade * Parallelized export functional for variant-oriented formats * Added means to write variant-list files as chunks when exporting * Minor changes * Individual-oriented exports now working in parallel * Minor change * Added mean to specify a location for export extraction files * Added mean to specify a location for export extraction files + fixed outputstream flush / close * All seems to be working fine * Minor changes * insertStep method in ProgressIndicator adds step at next position * Added safelyGetKnownAlleles() method which allows to fix incomplete known allele lists in VRD records * Replacing dots with underscores in metadata field names This used to cause trouble in the JSON document structure * Made taxon update immediately accounted for * add listReadableDbs in AbstractTokenManager * POM version update * Filter export data on project IDs if several projects in DB (faster export!) * Added some debug facility to GroupedExecutor * Improved debug info for GroupedExecutor * Minor change * Fixed chunk count problem with IGV exports * Minor changes * Minor changes * Moved VisualizationService class from Gigwa2ServiceImpl to Mgdb2Export * Made readToken method static --------- Co-authored-by: Alice Boizet <alice.boizet@cirad.fr>
2.8-RELEASE
Merged from staging for next release (#76) * feat: creation of files * on progress * dart on progress * waiting for examples files * on progress * feat: one row have to be tested * feat: 1row ok 2row seems ok but very long * feat: remove useless info + when no Chrom_ -> Chrom_Un * fix: ArrayList<String> genotypes -> String[] * fix: limit chrom_ to one word * fix: Chrom_Un -> Un * Made DartImport read data progressively (the whole file used to be loaded at once) * Minor fix * add information to vcf header * update DartInfo class * Update VCF info header description * fix importing metadata from BrAPI to manage the case of having several individuals or samples linked to the same externalRefId * fix intertek import - when importing genotypes with several samples for the same individual * Cancel ProgressIndicator removal if re-added before end of delay * fix storing extGermplasmDbId when several individuals with the same extGermplasmDbId, storing also extSampleDbId * Allowed to name individuals just like samples (for case without mapping) * Moved code for finding individual name to parent class ... and allowed for it to get the info from BrAPI * Allowed to create a SessionAttributeAwareThread from another * Minor change * Minor change * Added means to preload individual names from BrAPI by batch * Much refactoring to finalize direct BrAPI import, along with genotypes * Fixed bug occurring when special chars in hapmap header * Fixed NPE * Added means to preload individuals via BrAPI in Intertek import * save extRefId and extRefSource in externalReferences field * avoid saving twice the same extRefs in the case of having a second import from same endpoint * Fixed bug in scanning sample list in Intertek file * Added ExperimentalFeature interface * POM update --------- Co-authored-by: Yoan BIGGIO <yoan.biggio@epita.fr> Co-authored-by: Dorian Grasset <dorian.grasset@cirad.fr> Co-authored-by: Alice Boizet <alice.boizet@cirad.fr>