fix: inputs/.TNRS/schema.sql: taxon_match: added derived column "Accepted_species[_binomial]__@TNRS__@vegpath.org", which removes trailing whitespace
inputs/.TNRS/schema.sql: taxon_match: added derived column "matched~Name[_no_author]___@TNRS__@vegpath.org", which removes the "No suitable matches found." string
inputs/.TNRS/schema.sql: reordered derived columns in dependency order
fix: inputs/.TNRS/schema.sql: taxon_match: added derived column "Accepted_family__@TNRS__@vegpath.org", which is needed because "*Accepted_name_family" isn't always populated
inputs/.TNRS/schema.sql: taxon_match: put matched-taxon derived columns before accepted-taxon derived columns
inputs/.TNRS/data.sql: refreshed
lib/tnrs.py: switched to downloading all matches per name, as is needed to implement #917. note that this will break the parts of the schema that use the tnrs table, until Brad's match-picking algorithm can be implemented, but this tradeoff is necessary to be able to begin scrubbing sooner (Martha; wiki.vegpath.org/2014-05-29_conference_call#TNRS)
schemas/vegbien.sql: tnrs_input_name: don't scrub accepted names, as using multiple matches per name no longer provides a single accepted name to scrub. instead, the Accepted_* fields can be whitespace-split to generate the same columns that would have been generated by the scrubbing (and without the overhead of the extra TNRS call).
inputs/.TNRS/schema.sql: tnrs: populate match_num
inputs/test_taxonomic_names/_scrub/*: updated to TNRS schema
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/data.sql: re-ran TNRS using `inputs/test_taxonomic_names/test_scrub; rm=1 inputs/.TNRS/data.sql.run export_`
reran inputs/test_taxonomic_names/test_scrub, which generates the public.test_taxonomic_names sample schema
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).
Calls to `make inputs/.TNRS/cleanup`: Do `make inputs/.TNRS/tnrs_accepted/reinstall; make inputs/.TNRS/tnrs_other/reinstall` instead to use new split TNRS tables
inputs/test_taxonomic_names/_scrub/public.test_taxonomic_names.sql, TNRS.sql: Regenerated with schema and mappings changes
inputs/test_taxonomic_names/_scrub/public.sql, TNRS.sql: Regenerated with schema changes
inputs/test_taxonomic_names/test_scrub: Also export the results to inputs/test_taxonomic_names/_scrub/
