Song 559 change base schema

[rtisma]

Summary of changes

Related to #559

Renames:

• study to studyId
• file to files
• sample to samples
• donorGender to gender
• donorSubmitterId to submitterDonorId
• specimenSubmitterId to submitterSpecimenId
• sampleSubmitterId to submitterSampleId

Added:

• dataType to file object
• matchedNormalSubmitterSampleId to sample object and is required when specimen.tumourNormalDesignation == Normal. It is prohibited if specimen.tumourNormalDesignation != Normal
• tumourNormalDesgination to specimen object
• specimenTissueSource

Updated enum:

• gender enum from male, female, unspecified to Male, Female, Other
• specimenType to match whatever is in argo-clinical

Removed:

• specimenClass from baseSchema, however left column in DB as it cannot be automatically migrated (requires human intervention)

Misc:

• changed /upload endpoint to /submit, and UploadController/Service to SubmitController/Service
• cleaned up stale comments, and code
• added test for matchedNormal validation
• added V1__6 migration

Things that are not backwards compatible:

• specimenType is nullable because previous specimenType data does not follow the enum in db.
• same with tumourNormalDesignation and specimenTissueSource. These enforcements are entirely dependant on jsonSchema validation

[andricDu]

LGTM!