added inputs/CVS/verify/Review of CVS data in BIEN3-RKP2014Sept7.docx from Bob

added inputs/bien2_traits/_no_import since bien2_traits has been replaced by Cyrille_traits

added inputs/Cyrille_traits/

mappings/VegCore.htm: regenerated from wiki. made verbatimLocality a synonym of locality since they are used to store the same data.

fix: inputs/input.Makefile: $(nonHeaderSrcs): updated to exclude new header.txt

inputs/input.Makefile: added %/list_srcs

fix: lib/sh/util.sh: already_exists_msg(): changed calling convention to avoid it seeming like `return 0` is run if already_exists_msg() throws an error, when in fact already_exists_msg() is just a command that should be run before returning/errexiting

fix: inputs/input.Makefile: need to escape $ in commands, including inside comments

bugfix: inputs/input.Makefile: `$(call add*,$(svnFiles))` must be invoked externally to clear the $(wildcard) cache before expanding $(svnFiles)

inputs/VegBank/run*.log: updated. this adds the function call context in addition to the function location.

fix: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: make(): added warning that this will truncate the geoscrub database tables

added inputs/VegBank/run.call_graph.log

inputs/VegBank/run.log: updated for echo_vars() changes. the PG* vars, which contain important information, will now not need to be filtered out.

added inputs/VegBank/run.log

fix: inputs/input.Makefile: $(svnFilesGlob): *.log should be in both the subdirs and the main dir

inputs/input.Makefile: $(svnFilesGlob): *.log

inputs/Makefile: install: install an empty VegBIEN schema instead of all the datasources, at Mark's request. this enables loading just a single datasource.

added inputs/CVS/verify/Review of CVS data in BIEN3.docx

bugfix: inputs/input.Makefile: %/install: $(exportHeader) must come before postprocess because postprocess renames columns

bugfix: inputs/input.Makefile: $(import_install_): need `set -o pipefail` to enable errexit

inputs/.geoscrub/geoscrub_output/run: documented postprocess() rm=1 runtime (6 min)

fix: inputs/.geoscrub/geoscrub_output/postprocess.sql: map_geovalidity(): unscrubbable names should actually be geo*in*valid, not geovalid=NULL, according to Brad

bugfix: inputs/input.Makefile: sql/install: ";" for commands inside $(if) blocks need to be inside the $(if) block, too, because otherwise there will be dangling ";" without a statement (bash does not support empty statements containing just ";")

inputs/publishable datasources.xlsx: udpated

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_best_match_jerry_lu index to facilitate finding names affected by the match-picking bug (#943)

fix: inputs/HVAA/Specimen/postprocess.sql, map.csv: monthCollected/dayCollected: fix indefinite dates (which aren't supported by Postgres), as decided by Bob (https://docs.google.com/spreadsheets/d/1PI8n0CRttN7ttsXs5qfh5OFFzSoAfJj0gSbylgX6vj4/edit#gid=0)

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_name index

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_family index

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_species_binomial index

bugfix: mappings/VegCore-VegBIEN.csv: prefixed taxonomic ranks: use _concat_nullify() so that the prefix is only added if the epithet is non-NULL

bugfix: inputs/FIA/REF_RESEARCH_STATION/map.csv: mapped country, which is not provided in the FIA data

inputs/.TNRS/schema.sql: taxon_match: removed no longer used scrubbed_unique_taxon_name. the scrubbed name ranks are now generated from the other TNRS columns instead.

inputs/.TNRS/schema.sql: removed no longer used view ValidMatchedTaxon. use taxon_scrub instead.

inputs/.TNRS/schema.sql: taxon_scrub: use taxon_best_match directly, to avoid the need for a separate ValidMatchedTaxon view

fix: inputs/.TNRS/schema.sql: taxon_scrub: merged synonymous columns

schemas/vegbien.sql: taxon_scrub: documented steps to merge synonymous columns

inputs/.TNRS/schema.sql: removed no longer used view MatchedTaxon. use taxon_best_match instead.

inputs/.TNRS/schema.sql: ValidMatchedTaxon: use taxon_best_match now that it's equivalent to MatchedTaxon

fix: inputs/.TNRS/schema.sql: MatchedTaxon: merged synonymous columns

inputs/.TNRS/schema.sql: removed no longer used taxon_scrub.scrubbed_unique_taxon_name.* . use taxon_scrub instead.

inputs/.TNRS/schema.sql: taxon_scrub: use taxon_match derived columns instead of the incorrect values in taxon_scrub.scrubbed_unique_taxon_name.* (which does not work with the multi-match strategy)

inputs/.TNRS/schema.sql: MatchedTaxon: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.

inputs/.TNRS/schema.sql: taxon_scrub: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.

inputs/.TNRS/schema.sql: taxon_match: to port derived column changes to vegbiendev: derived_cols_export() code: documented runtime (6 h)

bugfix: inputs/.TNRS/schema.sql: removed no longer used derived column __accepted_infraspecific_label, which had a buggy formula that broke derived_cols_populate()

bugfix: inputs/.TNRS/schema.sql: removed no longer used derived column __accepted_infraspecific_label, which had a buggy formula that broke derived_cols_populate()

fix: inputs/.TNRS/schema.sql: taxon_match: to remove a column: updated instructions

**: updated to use the local machine's new hostname, frenzy

inputs/.TNRS/schema.sql: added new derived columns to derived views

fix: schemas/util.sql: derived_col_update(): also need steps to drop column, because DROP __ CASCADE doesn't work when there are dependent views

inputs/.TNRS/schema.sql: _accepted_infraspecific{rank,epithet}: use array slice of new _accepted{genus,specific_epithet,infra_{rank,epithet}}, which is simpler than using remove_prefix() in __accepted_infraspecific_label

inputs/.TNRS/schema.sql: "[accepted_]genus__@DwC__@vegpath.org": don't need to use *Accepted_name anymore because _accepted{genus,specific_epithet,infra_{rank,epithet}} is now generated from *Accepted_name

inputs/.TNRS/schema.sql: taxon_match."__accepted_{genus,specific_epithet}": renamed to "__accepted_{genus,specific_epithet,infra_{rank,epithet}}" since this now includes these other ranks as well

bugfix: inputs/.TNRS/schema.sql: taxon_match."__accepted_{genus,specific_epithet}": use "*Accepted_name" instead of "Accepted_species[_binomial]__@TNRS__@vegpath.org" (from "*Accepted_name_species") because Accepted_name_species apparently sometimes does not match the Accepted_name and uses malformed Unicode characters

inputs/.TNRS/schema.sql: taxon_match: `inputs/.TNRS/data.sql.run refresh`: documented runtime (1 min)

bugfix: inputs/.TNRS/schema.sql: taxon_match: use "Accepted_species[_binomial]__@TNRS__@vegpath.org" instead of "*Accepted_name_species". this fixes a bug in __accepted_infraspecific_label where Accepted_name_species with trailing whitespace could not be prefix-removed from names that contained just a species binomial.

fix: inputs/.TNRS/schema.sql: taxon_match: added derived column "Accepted_species[_binomial]__@TNRS__@vegpath.org", which removes trailing whitespace

inputs/.TNRS/schema.sql: added steps to remove a column and to add a non-derived column

inputs/.TNRS/schema.sql: taxon_match: to remove columns or add columns at the end: merged into "to add a new derived column"

inputs/.TNRS/schema.sql: to add columns in the middle: renamed to "to move a column to the middle" for clarity

inputs/.TNRS/schema.sql: to populate a new column: updated to use util.derived_col_update()

fix: inputs/.TNRS/schema.sql: taxon_match: to remove columns or add columns: also need to run util.recreate_view()

inputs/.TNRS/schema.sql: taxon_match: to remove columns or add columns at the end: don't need to run `rm=1 inputs/.TNRS/data.sql.run` because this is now run by `make schemas/remake`

inputs/.TNRS/schema.sql: added new derived columns to derived views

schemas/util.sql: remove_prefix(), remove_suffix(): support case-insensitive matching

bugfix: inputs/.TNRS/schema.sql: taxon_match.__accepted_infraspecific_label: need to use case-insensitive matching of the removed prefix because TNRS lowercases part of the Accepted_name

schemas/util.sql: remove_prefix(), remove_suffix(): support case-insensitive matching

bugfix: inputs/.TNRS/schema.sql: taxon_match: use wrapper for util.remove_prefix() so CHECK constraints that use it don't get dropped when the util schema is reinstalled

inputs/.TNRS/schema.sql: taxon_match: COMMENT: added steps to port derived column changes to vegbiendev

bugfix: inputs/.TNRS/schema.sql: taxon_match: derived columns: use new "matched~Name[_no_author]___@TNRS__@vegpath.org" instead of "*Name_matched" so that "No suitable matches found." is removed before concatenating with other fields

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

bugfix: inputs/.TNRS/schema.sql: "[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org": need to use "[accepted_]genus__@DwC__@vegpath.org" rather than "*Accepted_name" for this for rank = genus

inputs/.TNRS/schema.sql: taxon_match: added derived column "[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org"

bugfix: inputs/.TNRS/schema.sql: "[accepted_]genus__@DwC__@vegpath.org": need to populate this for rank = genus

inputs/.TNRS/schema.sql: taxon_match: added derived column "[scrubbed_]taxonomicStatus__@DwC__@vegpath.org"

bugfix: inputs/.TNRS/schema.sql: derived columns: use "Accepted_family__@TNRS__@vegpath.org" instead of "*Accepted_name_family" because "*Accepted_name_family" is sometimes missing

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

bugfix: inputs/.TNRS/schema.sql: taxon_match: to add columns in the middle: also need to run util.derived_cols_repopulate() since the dependency order has changed

fix: inputs/.TNRS/schema.sql: taxon_match: COMMENT: to add columns in the middle: also need to run util.derived_cols_update()

fix: inputs/.TNRS/schema.sql: taxon_match: COMMENT: updated util.derived_cols_sync() to util.derived_cols_update()

inputs/.TNRS/schema.sql: reordered derived columns in dependency order

inputs/.TNRS/schema.sql: reordered derived columns in dependency order

bugfix: schemas/util.sql: derived_cols_trigger_update(): need to clear derived cols first so old values won't be used in calculations

inputs/.TNRS/schema.sql: derived_cols_trigger_update(): put expr on same line as var, to save space

inputs/.TNRS/schema.sql: derived_cols_trigger_update(): removed lines between statements, which add too much space

fix: schemas/util.sql: derived_cols_trigger_update(): don't indent expr because may have multiple lines

bugfix: schemas/util.sql: derived_col_update(): set_comment(): vars can't have same name as params, which will be substituted

inputs/.TNRS/schema.sql: taxon_match: added derived column "[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org"

inputs/.TNRS/schema.sql: taxon_match: added derived column "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org"

inputs/.TNRS/schema.sql: added new derived columns to derived views

fix: schemas/util.sql: derived_col_update(): column comment: formula: put on own line to support multiline exprs

bugfix: schemas/util.sql: derived_col_update(): column comment: need to use expr from DB, not as provided by user, to avoid this changing when derived_col_update() is rerun

inputs/.TNRS/schema.sql: taxon_match: added derived columns scrubbed_*

inputs/.TNRS/schema.sql: taxon_match: put matched-taxon derived columns before accepted-taxon derived columns

inputs/.TNRS/schema.sql: taxon_match: added derived column "[matched_]species[_binomial]~(Accepted_)__@TNRS__@vegpath.org"

inputs/.TNRS/schema.sql: _matched_has_accepted: renamed to matched_has_accepted because the leading _ did not create vertical alignment anyway, due to different quoting syntaxes

schemas/util.sql: derived_col_update(): add steps to rename column

bugfix: schemas/util.sql: derived_col_update(): don't set_comment() until CHECK constraint exists so that we can use its canon-ed formula

inputs/.TNRS/schema.sql: taxon_match: added derived column _matched_has_accepted