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VegCSV-DwC merging¶
Check for inconsistent mappings¶
Add DwC mappings to VegCSV-VegBIEN.specimens.csv
:
bin/in_place mappings/VegCSV-VegBIEN.specimens.csv env all=1 bin/union mappings/DwC2-VegBIEN.specimens.csv;\
bin/in_place mappings/VegCSV-VegBIEN.specimens.csv bin/sort 0 1;\
bin/in_place mappings/VegCSV-VegBIEN.specimens.csv uniq
Check VegCSV-VegBIEN.specimens.csv
for VegCSV input terms that appear multiple times in a row If some of the output mappings are incompatible:
svn revert mappings/VegCSV-VegBIEN.specimens.csv
Edit the applicable mappings in mappings/VegCSV-VegBIEN.specimens.csv
and mappings/DwC2-VegBIEN.specimens.csv
make test
Commit
Continue with step 1, checking that the inconsistent multiple mappings have been merged into one mapping
Check for colliding mappings¶
Check VegCSV-VegBIEN.specimens.csv
for VegBIEN output XPaths that appear multiple times in a row Add an /_alt/#
suffix to each output XPath to specify which mapping should take priority when both input terms are present
Add VegCSV mappings to mappings/DwC2-VegBIEN.specimens.csv
¶
cp -p mappings/VegCSV-VegBIEN.specimens.csv mappings/DwC2-VegBIEN.specimens.csv
Open mappings/DwC2-VegBIEN.specimens.csv
and change VegCSV[DwC]
to DwC
make test
Check that tests pass
If not:
Add VegCSV mappings to DwC2
make test
Accept tests
Commit
Continue with step 1
Replace occurrences of DwC and VegCSV with Veg+ (or sometimes VegCore)¶
Rename the maps using svn mv
: (order matters)
# DwC2-VegBIEN.specimens.csv
svn mv mappings/DwC2-VegBIEN.specimens.csv mappings/VegCore-VegBIEN.specimens.csv
svn mv mappings/.DwC2-VegBIEN.specimens.csv.last_cleanup mappings/.VegCore-VegBIEN.specimens.csv.last_cleanup
svn mv mappings/for_review/DwC2-VegBIEN.specimens.csv mappings/for_review/VegCore-VegBIEN.specimens.csv
# DwC1-DwC2.specimens.csv
svn mv mappings/DwC1-DwC2.specimens.csv mappings/Veg+-VegCore.specimens.csv
svn mv mappings/.DwC1-DwC2.specimens.csv.last_cleanup mappings/.Veg+-VegCore.specimens.csv.last_cleanup
svn mv mappings/for_review/DwC1-DwC2.specimens.csv mappings/for_review/Veg+-VegCore.specimens.csv
# DwC-VegBIEN.specimens.csv
svn mv mappings/DwC.cs-VegBIEN.specimens.csv mappings/Veg+.cs-VegBIEN.specimens.csv
svn mv mappings/DwC-VegBIEN.specimens.csv mappings/Veg+-VegBIEN.specimens.csv
# VegX-VegCSV.stems.csv
svn mv mappings/VegX-VegCSV.stems.csv mappings/VegX-VegCore.stems.csv
svn mv mappings/.VegX-VegCSV.stems.csv.last_cleanup mappings/.VegX-VegCore.stems.csv.last_cleanup
svn mv mappings/for_review/VegX-VegCSV.stems.csv mappings/for_review/VegX-VegCore.stems.csv
# VegCSV-VegBIEN.specimens.csv
svn rm mappings/VegCSV-VegBIEN.specimens.csv
svn rm mappings/.VegCSV-VegBIEN.specimens.csv.last_cleanup
svn rm mappings/for_review/VegCSV-VegBIEN.specimens.csv
# VegCSV-VegBIEN.*.csv
for map in mappings/VegCSV-VegBIEN.*.csv; do rm "$map"; ln -s Veg+-VegBIEN.specimens.csv "$map"; done
for map in mappings/VegCSV-VegBIEN.{plots,organisms,stems}.csv; do svn mv "$map" "${map/VegCSV/Veg+}"; done
# *.self.*.csv
svn mv mappings/DwC.self.specimens.csv mappings/Veg+.self.specimens.csv
for map in mappings/VegCSV.self.{plots,organisms,stems}.csv; do svn rm "$map"; svn cp mappings/Veg+.self.specimens.csv "${map/VegCSV/Veg+}"; done
# inputs/*/maps/{DwC,VegCSV}.*.csv
for map in inputs/*/maps/{,.}DwC.*.csv{,.last_cleanup}; do svn mv "$map" "${map/DwC/Veg+}"; done
for map in inputs/*/maps/{,.}VegCSV.*.csv{,.last_cleanup}; do svn mv "$map" "${map/VegCSV/Veg+}"; done
Remove .last_cleanup
files: find . -name "*.last_cleanup" -delete
Change all map roots to Veg+
, including in mappings/roots
Change mappings/Makefile with the new map names, and add +
to $(filenameVia)
make mappings/
svn add mappings/VegCore.self.specimens.csv
There was never a corresponding mappings/DwC2.self.specimens.csv
because it was manually prevented from being created by a regexp filter. There is no harm in having one, and the filter should eventually be removed.
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