Validation

[benjaminran]

Should verify specimen type values with accepted codelist values.

Should verify that submitter specimen id and specimen sample id values are all distinct (never the same value in both columns).

Should warn if required jars not found.

[benjaminran]

Specifically, Submitter Specimen Type values should conform to the icgc specimen.0.specimen_type.v3 codelist (search 'specimen_type'). It's reproduced below:

specimen.0.specimen_type.v3

• 101 Normal - solid tissue
• 102 Normal - blood derived
• 103 Normal - bone marrow
• 104 Normal - tissue adjacent to primary
• 105 Normal - buccal cell
• 106 Normal - EBV immortalized
• 107 Normal - lymph node
• 108 Normal - other
• 109 Primary tumour - solid tissue
• 110 Primary tumour - blood derived (peripheral blood)
• 111 Primary tumour - blood derived (bone marrow)
• 112 Primary tumour - additional new primary
• 113 Primary tumour - other
• 114 Recurrent tumour - solid tissue
• 115 Recurrent tumour - blood derived (peripheral blood)
• 116 Recurrent tumour - blood derived (bone marrow)
• 117 Recurrent tumour - other
• 118 Metastatic tumour - NOS
• 119 Metastatic tumour - lymph node
• 120 Metastatic tumour - metastasis local to lymph node
• 121 Metastatic tumour - metastasis to distant location
• 122 Metastatic tumour - additional metastatic
• 123 Xenograft - derived from primary tumour
• 124 Xenograft - derived from tumour cell line
• 125 Cell line - derived from tumour
• 126 Primary tumour - lymph node
• 127 Metastatic tumour - other
• 128 Cell line - derived from xenograft tumour