Tidy up

[julie-sullivan]

A few small changes

• [x] Regulatory_region.test.json is in root. Is this used? If so, can we put in 'resources'? The commit message says that it's used to fix a test.
• [x] cellbase-mongodb/src/test/resources - should be moved to cellbase-lib
• [ ] old pull requests
• [x] old branches
• [ ] remove deprecated classes and tests
• [x] remove old Groovy and Spock tests
• [ ] cellbase-core.common - lots of these are in biodata. confirm they are there and delete.
• [x] cache in VariantAnnotationCalculator is not used. delete method.

[julie-sullivan]

[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java:[33,57] org.opencb.cellbase.lib.builders.clinical.variant.ClinVarParser in org.opencb.cellbase.li
b.builders.clinical.variant has been deprecated                                                                                                                                                                                      
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java:[35,57] org.opencb.cellbase.lib.builders.clinical.variant.CosmicParser in org.opencb.cellbase.lib
.builders.clinical.variant has been deprecated                                                                                                                                                                                       
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/BuildCommandExecutor.java:[36,57] org.opencb.cellbase.lib.builders.clinical.variant.GwasParser in org.opencb.cellbase.lib.$
uilders.clinical.variant has been deprecated                                                                                                                                                                                         
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/DownloadCommandExecutor.java:[49,98] verbose in org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOptions has been 
deprecated                                                                                                                                                                                                                           
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[122,116] verbose in org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOption$
 has been deprecated                                                                                                                                                                                                                 
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[163,48] Config(int,int,int,boolean) in org.opencb.commons.run.ParallelTaskRunner.Con$
ig has been deprecated                                                                                                                                                                                                               
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[164,36] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.co$
mons.run.ParallelTaskRunner has been deprecated                                                                                                                                                                                      
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[193,36] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.co$
mons.run.ParallelTaskRunner has been deprecated                                                                                                                                                                                      
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[195,32] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.co$
mons.run.ParallelTaskRunner has been deprecated                                                                                                                                                                                      
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[240,40] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.co$
mons.run.ParallelTaskRunner has been deprecated                                                                                                                                           
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[244,52] Config(int,int,int,boolean) in org.opencb.commons.run.ParallelTaskRunner.Con$
ig has been deprecated                                                                                                                                                                         
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[258,44] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.co$
mons.run.ParallelTaskRunner has been deprecated                                                                                                                                                                  
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[260,56] Config(int,int,int,boolean) in org.opencb.commons.run.ParallelTaskRunner.Con$
ig has been deprecated                                                                                                                                                                                                            
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[392,36] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.co$
mons.run.ParallelTaskRunner has been deprecated                                                                                                                                                                
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[393,32] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.co$
mons.run.ParallelTaskRunner has been deprecated                                                                                                                                               
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[780,51] phased in org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantA$
notationCommandOptions has been deprecated                                                                                                                                                          
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/VariantAnnotationCommandExecutor.java:[781,83] phased in org.opencb.cellbase.app.cli.main.CellBaseCliOptionsParser.VariantA$
notationCommandOptions has been deprecated                                                                                                                                                         
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/annotation/CellBaseWSVariantAnnotator.java:[114,50] getSourceEntries() in org.opencb.biodata.models.variant.Variant has been deprecat$
d                                                                                                                                                                                                    
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/annotation/CellBaseWSVariantAnnotator.java:[114,78] getAttributes() in org.opencb.biodata.models.variant.StudyEntry has been deprecat$
d                                                                                                                                                                                                                                    [WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/annotation/BenchmarkTask.java:[38,27] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.commons.run.ParallelT$ skRunner has been deprecated                                                                                                                                                                                       
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/annotation/VariantAnnotatorTask.java:[33,27] org.opencb.commons.run.ParallelTaskRunner.TaskWithException in org.opencb.commons.run.Pa$
allelTaskRunner has been deprecated                                                                                                                                                                                     
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/QueryCommandExecutor.java:[51,92] verbose in org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOptions has been dep$
ecated
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/executors/QueryCommandExecutor.java:[124,89] getGenomicSequence(org.opencb.commons.datastore.core.Query,org.opencb.commons.datastore.$ore.QueryOptions) in org.opencb.cellbase.core.api.GenomeDBAdaptor has been deprecated
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/main/annotation/VariationDataReader.java:[77,40] inferType(java.lang.String,java.lang.String) in org.opencb.biodata.models.variant.Variant has been deprecated
[WARNING] /home/julie/git/cellbase/cellbase-app/src/main/java/org/opencb/cellbase/app/cli/admin/executors/PostLoadCommandExecutor.java:[44,98] verbose in org.opencb.cellbase.app.cli.CliOptionsParser.CommonCommandOptions has been
deprecated