mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed infraspecificEpithet (Infraspecific_epithet_matched) to taxon at the infraspecies rank

mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed taxonomic ranks to the tree of life in the taxon table

schemas/vegbien.sql: taxon: Added comment that this table stores the tree of life

mappings/VegCore-VegBIEN.csv: accepted taxonomic terms: Use new _set_canon_taxonpath() to set the canon_taxonpath_id after the taxonpath has been inserted, so that if the taxonpath is an accepted name (scrubs to itself), it will link up to the just-inserted taxonpath with the taxonomic ranks parsed out, rather than to a new taxonpath containing only the few taxonomic ranks of the accepted name that TNRS provides. In particular, this (together with the tnrs_accepted_names sorting index on TNRS.tnrs) ensures that an accepted name is imported with its genus and species parsed out by TNRS instead of concatenated together in the Accepted_name_species field (genus+species). This enables the individual taxonomic ranks to be used in constructing the leaves of the tree of life (the taxon table).

sql_io.py: put_table(): Fixed bug where row_ct_ref was incorrectly being incremented when the iteration is a function call. This bug only occurred in row-based mode, because the DB cursor for a function call is not stored in column-based mode.

inputs/.TNRS/tnrs/map.csv: Use Name_matched_author/Name_matched_accepted_family instead of Author_matched/Family_matched because these fields are provided more often, due to being determined from the matched name itself rather than from the original string. This helps to fill in as many fields as possible. For accepted names (which scrub to themselves), this is especially important, because it adds the accepted name's family, which is not present in the input taxonomic name.

xml_func.py: process(): Fixed bug where need to preserve complex functions that have unevaluated XML nodes as arguments, because XML nodes are not accepted by sql_io.put() (they are handled by db_xml.put())

schemas/vegbien.sql: Renamed set_canon_taxonpath() to _set_canon_taxonpath() (adding _ prefix) so that db_xml.put() treats its arguments as arguments rather than as children with fkeys to parent

schemas/vegbien.sql: Added set_canon_taxonpath() to set a taxonpath's canon_taxonpath_id after it has been created

Added inputs/.TNRS/tnrs/cleanup.sql to cluster TNRS.tnrs on tnrs_accepted_names. This keeps TNRS.tnrs sorted with the accepted names first.