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# Date Author Comment
13853 06/25/2014 04:28 PM Aaron Marcuse-Kubitza

inputs/.TNRS/data.sql: refreshed

13850 06/25/2014 03:33 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: renamed to tnrs_match to distinguish it from other TNRS-related tables

13591 06/02/2014 04:50 AM Aaron Marcuse-Kubitza

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)

13590 06/02/2014 04:35 AM Aaron Marcuse-Kubitza

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).

13579 05/31/2014 10:28 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: populate match_num

13573 05/31/2014 08:10 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: added match_num

11970 01/20/2014 11:33 AM Aaron Marcuse-Kubitza

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).

11708 11/21/2013 08:48 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql, data.sql: updated for PostgreSQL 9.3

11643 11/10/2013 07:02 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: removed no longer used Accepted_scientific_name. use scrubbed_unique_taxon_name instead.

11630 11/10/2013 01:23 PM Aaron Marcuse-Kubitza

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.

11629 11/10/2013 01:19 PM Aaron Marcuse-Kubitza

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).

11628 11/10/2013 01:06 PM Aaron Marcuse-Kubitza

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

11627 11/10/2013 09:44 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: removed no longer used Max_score. use is_valid_match to determine validity instead.

11626 11/10/2013 12:09 AM Aaron Marcuse-Kubitza

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

11625 11/10/2013 12:08 AM Aaron Marcuse-Kubitza

inputs/.TNRS/data.sql: updated for new derived columns

10786 08/27/2013 10:14 PM Aaron Marcuse-Kubitza

inputs/.TNRS/data.sql: re-ran TNRS using `inputs/test_taxonomic_names/test_scrub; rm=1 inputs/.TNRS/data.sql.run export_`

10783 08/27/2013 09:53 PM Aaron Marcuse-Kubitza

inputs/.TNRS/data.sql: generate from the DB using `rm=1 inputs/.TNRS/data.sql.run export_` instead of being a hand-edited file

10746 08/27/2013 12:25 PM Aaron Marcuse-Kubitza

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.

9972 06/20/2013 08:03 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: added Is_homonym derived col (uses IRMNG.family_homonym_epithet, genus_homonym_epithet)

9762 06/06/2013 02:42 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: updated for current TSV schema: renamed Accepted_species->Accepted_name_species, Accepted_family->Accepted_name_family

9529 05/23/2013 03:33 PM Aaron Marcuse-Kubitza

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.)

9493 05/21/2013 07:37 PM Aaron Marcuse-Kubitza

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).

7855 03/06/2013 02:18 PM Aaron Marcuse-Kubitza

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

7293 01/18/2013 07:38 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: Added Max_score column for use in filtering out names that will be rejected by taxondetermination's constraints

7133 01/09/2013 09:57 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: Added Accepted_scientific_name field which will contain the joined-together accepted name that gets re-parsed by TNRS

5811 10/26/2012 04:34 PM Aaron Marcuse-Kubitza

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