VegX to VegCSV¶

• Table of contents
• VegX to VegCSV
  • DwC terms for VegX elements
  • Steps to switch VegX mappings to VegCSV

DwC terms for VegX elements¶

Total: 33

• catalogNumber
• class
• continent
• coordinateUncertaintyInMeters
• country
• county
• decimalLatitude
• decimalLongitude
• eventDate
• family
• fieldNotes
• fieldNumber
• footprintWKT
• genus
• identificationQualifier
• individualCount
• infraspecificEpithet
• kingdom
• locality
• locationID
• maximumDepthInMeters
• maximumElevationInMeters
• minimumDepthInMeters
• minimumElevationInMeters
• occurrenceID
• order
• phylum
• samplingProtocol
• scientificName
• scientificNameAuthorship
• specificEpithet
• stateProvince
• verbatimElevation

Steps to switch VegX mappings to VegCSV¶

• Note that now, mappings/VegX-VegCSV.stems.csv itself will not be in use, but can be used towards a new CTFS mapping

1. Create mappings/for_review/VegBIEN-DwC2.specimens.csv by inverting mappings/for_review/DwC2-VegBIEN.specimens.csv
2. Create mappings/VegX-VegCSV.stems.csv:
   

   make mappings/VegX-VegCSV.stems.csv-remake
   

3. In mappings/VegX-VegCSV.stems.csv's output column:
   1. Resolve ambiguous names that appear twice
   2. Search-and-replace simplified XPaths with standardized names
   3. Make maps that depend on it: make mappings
4. Rename all inputs' VegX maps to VegCSV:
   

   shopt -s nullglob
   for dir in inputs/*/maps/; do
       (cd $dir && { for map in VegX*.csv; do svn mv "$map" "${map/VegX/VegCSV}" || break; done; }) || break
   done
   

5. For each input:
   1. Create VegCSV.<table>.csv by joining what was VegX.<table>.csv to VegX-VegCSV.stems.csv:
      

      for map in inputs/*/maps/VegCSV.{plots,organisms,stems}.csv; do
          bin/in_place "$map" env only_one=1 map_1_core_only=1 quiet=1 bin/join mappings/VegX-VegCSV.stems.csv || break
          bin/in_place "$map" bin/cols 0 1 2 || break
      done
      

6. Clean up the changed maps: make
7. Check that the test outputs have only minor additions (due to merging of some previously separate XPaths): make test
8. svn add inputs/*/maps/.*.last_cleanup
9. In mappings/VegX-VegCSV.stems.csv, remove user-defined VegX terms, which will no longer be in use
   

   bin/in_place mappings/VegX-VegCSV.stems.csv grep -vF simpleUserdefined