Integrate sample CSV format with other objects and format JSON accordingly

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Description

Current sample CSV files are reflected in MongoDB as:

{
  _id: ObjectId("61cc60955dba44e035c9533e"),
  title: "test sample",
  alias: "test1",
  description: "A test sample metadata based on the EGA submitter portal format",
  subjectId: "123456789abc",
  bioSampleId: "",
  caseOrControl: "",
  gender: "unknown",
  organismPart: "",
  cellLine: "",
  region: "",
  phenotype: "some disease state",
  sampleName: {
    taxonId: 9606
  },
  accessionId: "8976b3e507034027992f45179b4c00b1",
  dateCreated: Date("2021-12-29T13:20:21.757Z"),
  dateModified: Date("2021-12-29T13:20:21.757Z")
}

which does not reflect relevant information according to the JSON schema.

For this information to be relevant we would need to adjust the CSV files to work with analysis/ runs objects (similar to #321 ) and with EGA analysis CSV files
samples-bam.csv
samples-complete-genomics.csv
samples-cram.csv
samples-fasta.csv
samples-one-fastq-file-single.csv
samples-pacbio-hdf5.csv
samples-sff.csv
samples-srf.csv
samples-two-fastq-files-paired.csv

DoD (Definition of Done)

Integrate sample and analysis so that the data submitted via CSV is useful for users.

Testing

Unit and integration testing.