*{.sh,run}: runscript targets: use begin_target instead of echo_func so the target name is properly echoed. note that this requires using with_rm so that $rm is properly progagated to applicable invoked targets. (previously, $rm was progagated to all invoked targets. note that with_rm only works inside a runscript target that starts with begin_target.)
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_`
inputs/test_taxonomic_names/_scrub/TNRS_results.ppt: highlighted the sample row and related rows
inputs/test_taxonomic_names/_scrub/TNRS_results.xls: moved arrows to TNRS_results.ppt so they can be changed more easily
inputs/test_taxonomic_names/_scrub/TNRS_results.ppt: TNRS.tnrs: added diagram labels for the various names and steps
inputs/test_taxonomic_names/_scrub/TNRS_results.xls: use "Poa annua var. eriolepis"->"Poaceae Poa annua L." as the synonym example instead of "Poa annua fo. lanuginosa"->"Poaceae Poa annua var. annua" because the input name is simpler and it's closer to the beginning of the list
inputs/test_taxonomic_names/_scrub/run: exports/make(): tnrs.csv: include Name_matched instead of Genus_matched+Specific_epithet_matched because this also contains lower ranks, which are used in the TNRS synonymizing
inputs/test_taxonomic_names/_scrub/TNRS_results.ppt: added annotations explaining the import steps
added inputs/test_taxonomic_names/_scrub/TNRS_results.ppt, containing the *.png screenshots with tables labeled
added inputs/test_taxonomic_names/_scrub/*.png, screenshots of the TNRS_results.xls tabs (LibreOffice does not preserve the formatting when pasting a spreadsheet to a PowerPoint as a table, and the table editing options are limited)
added inputs/test_taxonomic_names/_scrub/TNRS_results.xls with formatted versions of the *.csv tables
inputs/test_taxonomic_names/_scrub/run: exports/make(): subset the columns to include only the most important to demo how the data is represented
inputs/test_taxonomic_names/_scrub/run: exports/make(): allow specifying an explicit columns list for each table using cols=... (initially set to all columns)
added inputs/test_taxonomic_names/_scrub/*.csv exports
added inputs/test_taxonomic_names/_scrub/run, which exports the test_scrub-populated tables to CSV
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/test_scrub: Fixed bug where public.sql export did not include the "CREATE SCHEMA public" statement, because pg_dump doesn't add it to backups, by using new schemas/rename/% make target to first rename the public schema and then exporting it
inputs/test_taxonomic_names/_scrub/public.sql, TNRS.sql: Regenerated with schema changes
inputs/test_taxonomic_names/_scrub/public.sql: Regenerated with schema changes
inputs/test_taxonomic_names/test_scrub: Also export the results to inputs/test_taxonomic_names/_scrub/
