moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).
inputs/.TNRS/: Moved no longer needed public.unscrubbed_taxondetermination_view/ to _archive/
mappings/VegCore.htm: Regenerated from wiki. Documentation has been added on how to choose term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming) and how to form globally unique ID values (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Forming-IDs). Source and Specimen terms have been renamed to be self-explanatory and unambiguous (the DwC equivalents remain as synonyms). Short definitions of Source terms have been added to explain the differences between them. Source, Specimen, and Collection terms have been shortened according to the new instructions for choosing preferred term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming).
mappings/VegCore.csv: Regenerated from wiki. This causes TNRS's Annotations (cf/aff) to be mapped into VegBIEN.
mappings/VegCore-VegBIEN.csv: matched*Fit_fraction: Remapped to taxonconfidence instead of taxonfit
mappings/VegCore-VegBIEN.csv: Also include morphospecies in the accepted taxondetermination's taxonverbatim, so that it can easily be retrieved by the analytical DB views
mappings/VegCore-VegBIEN.csv: Don't create NCBI crosslinks for the matched taxonomic name. These crosslinks are no longer needed now that TNRS provides a separate accepted name on which crosslinks can be made.
schemas/vegbien.sql: unscrubbed_taxondetermination_view: Include the accepted name's row next to the matched name's row instead of merging the two together into one TNRS row, to allow including separate taxondeterminations for the matched and accepted names. Added Max_score from TNRS.tnrs.
mappings/VegCore-VegBIEN.csv: Mapped accepted* taxonomic name, now to separate accepted taxondetermination
schemas/vegbien.sql: taxondetermination_set_iscurrent(): Changed TNRS determinationtype from computer to matched, to allow for a separate accepted determinationtype
schemas/vegbien.sql: taxonlabel: Removed creationdate, which duplicates taxondetermination.determinationdate
mappings/VegCore-VegBIEN.csv: Removed no longer used mappings for verbatimScientificName in _if conditions
mappings/VegCore-VegBIEN.csv: Removed no longer used accepted and verbatim (parsed) taxonlabels, which have been replaced by a single accepted or matched taxondetermination created by scrub.make
mappings/VegCore-VegBIEN.csv: Removed TNRS input taxonlabels meant to cross-link to taxonlabels added by the TNRS import, because TNRS taxondeterminations are now created instead
mappings/VegCore-VegBIEN.csv: main taxonverbatim.morphospecies "if has verbatim name" condition: Fixed bug where need to remove the taxonIsCanonical flag, because the TNRS.public.unscrubbed_taxondetermination_view table (which uses this flag) should include this field (although not other places where the morphospecies is stored by other TNRS tables)
mappings/VegCore-VegBIEN.csv: primary taxonlabel's parent taxonlabel: Fixed bug where a taxonverbatim was incorrectly being created solely to store the taxonRank, even though it was already stored in the taxonlabel's rank field
mappings/VegCore-VegBIEN.csv: Don't map morphospecies to the parsed taxonlabel's taxonepithet, because this causes an extra, parsed taxonlabel to be created for TNRS.public.unscrubbed_taxondetermination_view. It is not needed by the other TNRS tables.
inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Omit Infraspecific_rank to help avoid creating a separate, parsed taxonlabel. Don't map to taxonRank because Name_matched_rank is populated more often.
schemas/vegbien.sql: Use new TNRS.tnrs_canon instead of tnrs+accepted to avoid creating additional taxonlabels for the parsed, matched, and accepted names and instead just use the most-canonicalized name of the names output by TNRS (the accepted name if available, or the matched name otherwise)
mappings/VegCore-VegBIEN.csv: Remapped matched*Fit_fraction to taxondetermination.taxonfit when a taxondetermination, not just a taxonlabel, is provided
mappings/VegCore-VegBIEN.csv: taxonlabel.taxonomicname: Prepend the family to the rest of the name using new _merge_prefix() instead of _join_words()/_nullIf(), so that any input taxonomic name that includes the family will not have the family duplicated in the combined taxonomic name. Previously, the duplication was removed only when the rest of the input name was equal to the family. This change fixes a bug in the new TNRS import where a pre-concatenated taxonomic name (Accepted_scientific_name) which includes the family is now used instead of Accepted_name, which only includes it when it's equal to the family.
inputs/.TNRS/schema.sql: tnrs+accepted: Added new Accepted_scientific_name column and mapped it in public.unscrubbed_taxondetermination_view
mappings/VegCore-VegBIEN.csv: Also map the morphospecies to the accepted taxonverbatim when an accepted name is provided
inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Mapped Accepted_name.*
schemas/vegbien.sql: unscrubbed_taxondetermination_view: Use new tnrs+accepted instead of tnrs so that the accepted name can be imported at the same time
inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Set dateIdentified to _now()
mappings/VegCore-VegBIEN.csv: identificationType: Fixed bug in mapping where extra *_id/ needed to be removed
inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Set taxonOccurrenceID to dummy value 0 to enable the taxonoccurrence CHECK constraint to pass. This is needed because the constraint must pass before the pkey (which should already exist) is even checked.
inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Set identificationType to computer
Added inputs/.TNRS/public.unscrubbed_taxondetermination_view/
