Complete Follow Up Scripts Based Validations

[rosibaj]

Currently all scripts listed in the dictionary are placeholders. We need to update these to include real script based validation. An example script is here: https://wiki.oicr.on.ca/display/icgcargotech/Validation+Script+Template

For the follow_up schema (https://github.com/icgc-argo/argo-dictionary/blob/master/schemas/follow_up.json), please implement the following script based validations in the dictionary:

• 1) For the field relapse_interval , if disease_status_at_followup =relapse then this field must have a value.
• 2) For the field method_of_progression_status, if disease_status_at_followup =progression or relapse, then this field must have a value.
• 3) For the field anatomic_site_progression_or_recurrences, if disease_status_at_followup =progression or relapse, then this field must have a value
• 4) For the field, recurrence_tumour_staging_system, if disease_status_at_followup =progression or relapse, then this field must have a value.
• For the field, posttherapy_tumour_staging_system, if disease_status_at_followup =progression or relapse, then this field can have a value, otherwise it should not have a value.
• 3) Add the correct tags to the dictionary schemas so they will appear in the Dictionary viewer. A guide for tags can be found here: https://wiki.oicr.on.ca/pages/viewpage.action?pageId=134938807

[wajiha-oicr]

@rosibaj Regarding task 2), I'm looking at the code list and see two possible values that say 'progression'.

"codeList": [
          "Complete remission",
          "Distant progression",
          "Loco-regional progression ",
          "No evidence of disease",
          "Partial remission",
          "Relapse",
          "Stable"
        ]

Is it just those two values, or do you foresee more entries ending with 'progression' that would count for this script, and would warrant a regex?

[rosibaj]

@wajiha-oicr unknown - i dont forsee it, but it is possible to have more progression types in future.

[wajiha-oicr]

I'll make a regex to match values that end in progression for now, this may need to be modified if more progression types are added which do NOT satisfy the requirement

[wajiha-oicr]

blocked by #47