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/schema.sql, data.sql: updated for PostgreSQL 9.3
inputs/.TNRS/schema.sql: tnrs: removed no longer used Accepted_scientific_name. use scrubbed_unique_taxon_name instead.
inputs/.TNRS/schema.sql: tnrs: removed Is_homonym, since this did not take into account the never_homonym status (when the author disambiguates) or the ability of a non-homonym at a lower rank to override a homonym at a higher rank. taking these into account just produces the value of is_valid_match.
inputs/.TNRS/schema.sql: tnrs: removed Is_plant, since this functionality is now provided by is_valid_match. note that whether a name is a plant is not meaningful for TNRS, because it can match only plant names (thus a "non-plant" is actually a non-match).
inputs/.TNRS/schema.sql: tnrs: added scrubbed_taxon_name_with_author derived column, which uses the matched name when an accepted name is not available
inputs/.TNRS/schema.sql: tnrs: removed no longer used Max_score. use is_valid_match to determine validity instead.
bugfix: lib/runscripts/file.pg.sql.run: export_(): exclude Source and related tables so that these will be re-created by the staging tables installation instead, ensuring that they are always in sync with the Source/ subdir
inputs/.TNRS/data.sql: updated for new derived columns
inputs/.TNRS/data.sql: re-ran TNRS using `inputs/test_taxonomic_names/test_scrub; rm=1 inputs/.TNRS/data.sql.run export_`
inputs/.TNRS/data.sql: generate from the DB using `rm=1 inputs/.TNRS/data.sql.run export_` instead of being a hand-edited file
inputs/.TNRS/schema.sql: tnrs.Time_submitted: renamed to batch and added fkey to batch.id. this requires including the batch table in inputs/.TNRS/data.sql, so that the fkey is satisfied (batch entries are already added by bin/tnrs_db.
inputs/.TNRS/schema.sql: tnrs: added Is_homonym derived col (uses IRMNG.family_homonym_epithet, genus_homonym_epithet)
inputs/.TNRS/schema.sql: updated for current TSV schema: renamed Accepted_species->Accepted_name_species, Accepted_family->Accepted_name_family
inputs/.TNRS/schema.sql, data.sql: updated TNRS CSV columns to preserve Name_matched_accepted_family even though it isn't present in the current TNRS CSVs. this way, Name_matched_accepted_family can still be used for previously-scrubbed names, and family_matched can be added back to analytical_stem_view. (now that bin/tnrs_db uses an explicit columns list in COPY TO, the absence of a column in the CSV is no longer a problem.)
inputs/.TNRS/schema.sql, data.sql: updated for new TNRS CSV columns (see bug at https://pods.iplantcollaborative.org/jira/browse/TNRS-183). note that these columns may eventually change back (comment by Naim at https://pods.iplantcollaborative.org/jira/browse/TNRS-183#comment-34444).
inputs/.TNRS/data.sql: Re-ran TNRS on the test_taxonomic_names so that the sample data would contain all the accepted names under the current acceptedScientificName formula, and would not produce any entries for unscrubbed names in tnrs_input_name
inputs/.TNRS/schema.sql: tnrs: Added Max_score column for use in filtering out names that will be rejected by taxondetermination's constraints
inputs/.TNRS/schema.sql: tnrs: Added Accepted_scientific_name field which will contain the joined-together accepted name that gets re-parsed by TNRS
inputs/.TNRS/: Added data.sql containing the test_taxonomic_names TNRS results, so that a new installation of VegBIEN will contain the necessary data to make the tests pass, including the TNRS import test
