Change base schema of song

[rosibaj]

Description

The song base schema (those fields not dynamically decided by user submitted schemas) currently have some older data fields/concepts that do not match the latest data models.

The base schema needs some changes to the default required fields in teh song base schema.

Expected base/required fields

{
  "studyId": "RAWR-CA",
  "analysisType": {
    "name": "sequencing_experiment",
    "version": 3
  },
  "samples": [
    {
      "submitterSampleId": "tumour-sample-rosi-1",
       "matchedNormalSubmitterSampleId":"normal-sample-rosi-2",
      "sampleType": "DNA",
      "specimen": {
        "submitterSpecimenId": "specimen-rosi-1",
        "tumorNormalDesignation": "Tumour",
        "specimenTissueSource": "Primary tumour - solid tissue"
      },
      "donor": {
        "submitterDonorId": "donor-rosi-1",
        "gender": "Female"
      }
    }
  ],
  "files": [
    {
      "dataType": "Aligned Reads"
      "fileType": "BAM",
      "fileName": "this_is_a_file_name.bam",
      "fileSize": 133684363564,
      "fileMd5sum": "e4fe8353ae62045642a2124909c5cfa5",
      "fileAccess": "controlled"
    }
  ]
}

Summary of changes

These updates to the base SONG

• Change study to studyId
• Removing info fields from displaying at each level when not being used
• Rename sample to samples
• Rename file to files
• Rename /upload to /submit
• Adding dataType to base file entity
• Adding sample_type, tumor_normal_designation, and specimen_tissue_source
• Changing the naming schema to submitter__id e.g. submitter_donor_id,
  submitter_sample_id
• Updating the permissible values on the base fields to match the clinical submission system
• Making sample/files plural.
• Add matched_normal_submitter_sample_id as a base schema field ; @rosibaj confirm json schema with validation on tumour field

2019-12-17 update: the matched_normal_submitter_sample_id was moved to outside the specimen object, under sample. This can be completed with JSON schema, but requires only 2 options: Tumor or Normal to prevent complexity.
This field should ONLY be filled in on Tumor schema type