ecotaxa-darwin-core

Deno command-line tools for creating Darwin Core records from EcoTaxa exports.

ecotaxa-occurrences

$ ecotaxa-occurrences -h
Convert EcoTaxa data to Darwin Core Occurrences

Use:
  ecotaxa-occurrences --project {number} [OPTIONS] < INPUT

Options
  --project             EcoTaxa project number (integer)
  --dataset-id
  --country             Set country code
  --not-living          Also include records classified as not-living
  --dynamic-properties  Store all unknown variables in dynamicProperties
  --from                Set input format [ tsv | ndjson ]

Examples

Minimal example

$ curl -s https://raw.githubusercontent.com/akvaplan-niva/ecotaxa-darwin-core/main/testdata/ecotaxa-doi-export-1-line.tsv | ecotaxa-occurrences --project 818
{"scientificName":"Copepoda","organismQuantity":1,"organismQuantityType":"individuals","occurrenceStatus":"present","eventDate":"2017-08-31T11:11:11Z","fieldNumber":"n1_12m_dive_autumn_2017_large","catalogNumber":"n1_12m_dive_autumn_2017_large_tot_1_2","locality":"n1","basisOfRecord":"MachineObservation","verbatimEventDate":"20170831T111111","decimalLongitude":-14.78215,"decimalLatitude":78.375417,"maximumDepthInMeters":12,"minimumDepthInMeters":12,"samplingProtocol":"dive","sampleSizeValue":99999,"sampleSizeUnit":"m3","samplingEffort":"100 µm mesh","occurrenceID":"288a98e6-ee9f-5171-afaf-f9b61dd0af4d","datasetID":"16c02403-3bca-59d2-b057-c0c40958827b","eventID":"8753512a-b0bc-5480-a947-a9a0a5111853","parentEventID":"16c02403-3bca-59d2-b057-c0c40958827b","countryCode":"NO","geodeticDatum":"WGS84","coordinateUncertaintyInMeters":30,"dateIdentified":"2018-05-14T00:00:00Z","identificationVerificationStatus":"validated","identificationRemarks":"living>Eukaryota>Opisthokonta>Holozoa>Metazoa>Arthropoda>Crustacea>Maxillopoda>Copepoda","identifiedBy":"https://ecotaxa.obs-vlfr.fr | User Name"}

Test

deno test *test.js

Install

deno install https://raw.githubusercontent.com/akvaplan-niva/ecotaxa-darwin-core/main/ecotaxa-occurrences.js