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 <[email protected]>

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 <[email protected]>
Co-authored-by: Dorian Grasset <[email protected]>
Co-authored-by: Alice Boizet <[email protected]>

2.7-RELEASE

2.7-RELEASE

2.6.1-RELEASE

POM version update

2.6-RELEASE

POM update

2.5.1-RELEASE

POM update

2.5-RELEASE

POM version update

2.4.1-RELEASE

Storing sequence length when provided in VCF

2.4-RELEASE

Updated POM version

2.3-RELEASE

Upgraded mongo driver & spring data dependency versions