Add extinctFilter var to sector forms

[camiplata]

Could it be possible to create different sectors for PBDB base on extant and extinct taxa? As it has one of the highest priorities is adding names from extant taxa (not necessarily wrong) for groups like birds or insects where there are more curated sources.

[mdoering]

It is sth we could add, yes. But maybe it doesn't have to be such a high priority?

[camiplata]

no, is not a priority. But then I would like to move PBDB towards the end of the priority lists

[camiplata]

Another use case for the feature is IRMNG, as it has many fossil taxa that we would like to add.

CatalogueOfLife/data#737

[mdoering]

I will add a extinctFilter setting for sectors that accepted the 3 states null/true/false with true only syncing extinct usages.

[camiplata]

@mdoering where can I find the extinctFilter? I looked at the UI and the config file but I'n not sure how to set it up

[mdoering]

@camiplata only the UI is missing at this point. While we wait for @thomasstjerne to implement it you could use the API to update some sectors or let me know about the ones you want to be changed and I can do that for you

[camiplata]

Hi @mdoering, great could you plese help me setting up this two sectors:

• PDBD merge sector 54638 of dataset https://www.checklistbank.org/catalogue/3/dataset/1174/metadata
• IRMG merge sector 58671 of dataset https://www.checklistbank.org/catalogue/3/dataset/2007/metadata

[mdoering]

You can do this by retrieving a sector, modify its content, i.e. add the extinctFilter property above, and PUT it back to the API:

curl -s --user USER:PWD -X GET "https://api.checklistbank.org/dataset/3/sector/58671" > sector.json   
vi sector.json
curl -s --user USER:PWD -X PUT -H "Content-Type: application/json" --data-binary @sector.json "https://api.checklistbank.org/dataset/3/sector/58671"

[mdoering]

I have updated the 2 sectors above via the API:

% curl -s -X GET "https://api.checklistbank.org/dataset/3/sector/54638" | jq .  
{
  "created": "2024-08-16T19:39:27.078008",
  "createdBy": 728,
  "modified": "2025-01-17T14:26:06.455978",
  "modifiedBy": 101,
  "datasetKey": 3,
  "id": 54638,
  "subjectDatasetKey": 1174,
  "mode": "merge",
  "priority": 127,
  "extinctFilter": true,
  "copyAccordingTo": false,
  "removeOrdinals": false,
  "size": 0
}
curl -s -X GET "https://api.checklistbank.org/dataset/3/sector/58671" | jq .  
{
  "created": "2025-01-17T13:42:57.781129",
  "createdBy": 728,
  "modified": "2025-01-17T14:28:48.098273",
  "modifiedBy": 101,
  "datasetKey": 3,
  "id": 58671,
  "subjectDatasetKey": 2007,
  "mode": "merge",
  "priority": 128,
  "extinctFilter": true,
  "copyAccordingTo": false,
  "removeOrdinals": false,
  "size": 0
}