This is an implementation of a darwincore export, for one of the FCIG-OZCAM participants.

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There are three parts to the mapping:

• the main script (anfc_dwc.run.pl),
• main mapping script (anfc_dwc.map.pl),
• country/state/ocean values mapping (anfc_dwc.map-cntryocn.pl).

This document doesn't cover (refer to the data manager):

• method used to extract data from the texpress database
• method used to send data to the atlas

The first export component is a perl script, anfc_dwc.run.pl, which is the entry point for mapping a previously generated report to the simple-dwc format – this script takes instruction through the command line for various input/output options:

usage: anfc_dwc.run.pl <IN> <OUT> <ERROR> <LOG>
 - all 4 arguments:  input file (or 'STDIN'), output file (or 'STDOUT'), error file, log file
 - 3 arguments:      input file, output file, error file (run log to stdout)
 - 2 arguments:      input file, output file (errors stderr, run log to stdout)
 - 1 argument:       input file (output stdout, errors stderr, no run log)
 - no arguments:     (input stdin, output stdout, errors stderr, no run log)

After establishing a valid environment it reads from the input stream and expects to find a header row followed by data rows. The field delimiter is defined in the script variable $reDelim (currently the sequence +| "plus pipe") and is used by the perl split() function to separate rows into fields for processing in the mapping scripts.

Each row is mapped individually, as it is encountered in the source file, via the map_record() function defined in anfc_dwc.map.pl. Mapping results - stored in a temporary variable @arr_output - are printed to the output stream (if possible) and any warnings or errors encountered during the mapping are stored in the %hErrors buffer. Under successful conditions the script also prints periodically to the log stream, with any error rows being specifically marked as well. At the end of input processing, the contents of the error buffer are flushed to the error stream in a structured format.

Activity diagram for https://github.com/AtlasOfLivingAustralia/ala-datamob/tree/master/biodomains/fcig-ozcam/anfc/anfc_dwc.run.pl

Details on the steps in the previous diagram correspond with activity in anfc_dwc.map.pl:

• 5.1 - map constants and 1:1 fields -
  
  • dwc.typestatus, (dwc.typename, dwc.typeauthor, dwc.typeyear)
    
  • dwc.basisOfRecord, dcterms:type
    
  • dcterms:rightsHolder, dwc.institutionCode, dwc.collectionId
    
  • dwc.occurrenceStatus
    
  • dwc.family, dwc.genus, dwc.specificEpithet, dwc.infraspecificName, dwc.scientificName
    
  • dwc.minimumdepth, dwc.maximumdepth

• 5.2 - map dwc.country, dwc.stateProvince, dwc.waterBody and dwc.verbatimLocality:
  (see anfc_dwc.map-cntryocn.pl for map_find_*)
  
  • if country doesn't equal 'yes', 'no' or 'unknown'
    
    1. warning is logged
       
    2. dwc.verbatimLocality, dwc.country, dwc.stateProvince and dwc.waterBody unpopulated
       
  • if country equals 'yes' :
    
    1. dwc.country set to 'Australia'
       
    2. test state_territory against map_find_state(): success to dwc.stateProvince
    3. dwc.verbatimLocality populated with source data
       
    4. dwc.waterBody unpopulated
       
  • if country equals 'no' :
    
    1. test state_territory against map_find_country(): success to dwc.country
    2. otherwise, test state_territory against map_find_ocean(): success to dwc.waterBody
    3. otherwise, warning is logged
       
    4. dwc.verbatimLocality populated with source data
       
    5. dwc.stateProvince unpopulated
       
  • if country equals 'unknown' :
    
    1. test state_territory against map_find_ocean(): success to dwc.waterBody
    2. dwc.verbatimLocality populated with source data
       
    3. dwc.country and dwc.stateProvince unpopulated

• 5.3 - map dwc.catalogNumber, dwc.otherCatalogNumbers, dwc.occurrenceId, dcterms:modified and dwc.verbatimModified, dwc.eventDate and dwc.verbatimEventDate

• 5.4 - see map_coords()

• dwc.decimalLatitude, dwc.decimalLongitude
• dwc.footprintWKT
• dwc.coordinatePrecision
• note: dwc.verbatimLatitude and dwc.verbatimLongitude are populated with source data by map_record() regardless of result

Activity diagram for https://github.com/AtlasOfLivingAustralia/ala-datamob/tree/master/biodomains/fcig-ozcam/anfc/anfc_dwc.map.pl map_coords() function