Standard outputs from TAF repos (ARTEFACTS)

[colinpmillar]

Summary

Please see the following proposal for defining standard outputs from a TAF analysis.

In order to identify standard outputs from stock assessments, we need to define a set of 'output types' and these should belong to a vocabulary

Proposal for new code type: CodeType: TAFOutputTypes - standard outputs from TAF analyses

Codes:

• SAG - file formatted for upload to SAG
• ASD - file formatted for upload to ASD
• FLStock - RData file containing a single FLStock object

Other potential codes (draft)

• RDBESnational
• RDBESsummary

An example of usage in a TAF analysis - the user creates a file called ARTIFACTS.json, this file contains an array of outputs, and the creation of the file will be supported by R functions in icesTAF package. The file contains an array of entries with three elements

{
  "file": string,
  "type": vocab - TAFOutputTypes ,
  "metdata": [
    {
      "code_type": string - vocab code type,
      "code": string - vocab code within code_type
    }
  ]
}

for example:

[
{
  "file": "output/sag_upload.xml",
  "type": "SAG",
  "metdata": [
    {
      "code_type": "ICES_StockCode",
      "code": "san.sa.6"
    },
    {
      "code_type": "Year",
      "code": "2023"
    }
  ]
},
{
  "file": "output/asd_upload.xml",
  "type": "ASD",
  "metdata": [
    {
      "code_type": "ICES_StockCode",
      "code": "san.sa.6"
    },
    {
      "code_type": "Year",
      "code": "2023"
    }
  ]
},
{
  "file": "output/stock.RData",
  "type": "FLStock",
  "metdata": [
    {
      "code_type": "ICES_StockCode",
      "code": "san.sa.6"
    },
    {
      "code_type": "Year",
      "code": "2023"
    }
  ]
}
]

Each output type will be decorated with metadata, depending on the output type different metadata will be required. We need to manage the definition of output types somewhere. The definition at its simplest can be: output type definition:

• name: e.g. SAG
• meta data code types required: e.g. stockCode, Year (could also be: assessmentPurpose http://vocab.ices.dk/?codetypeguid=df07b00e-80b9-44cd-8fc1-6fd35d4a1777)

We may also want to add to the definition:

• license
• validity check function: an R function returning TRUE if valid
• QC report: a short R markdown script return an html QC report on the file