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# Date Author Comment
14588 08/26/2014 05:02 PM Aaron Marcuse-Kubitza

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

14582 08/26/2014 04:07 PM Aaron Marcuse-Kubitza

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

14579 08/26/2014 02:52 AM Aaron Marcuse-Kubitza

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

14556 08/21/2014 07:31 PM Aaron Marcuse-Kubitza

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

14532 08/20/2014 04:26 PM Aaron Marcuse-Kubitza

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 ";")

14512 08/19/2014 11:47 AM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: udpated

14492 08/18/2014 01:58 PM Aaron Marcuse-Kubitza

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)

14490 08/17/2014 07:49 AM Aaron Marcuse-Kubitza

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)

14468 08/11/2014 07:48 AM Aaron Marcuse-Kubitza

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

14467 08/11/2014 07:46 AM Aaron Marcuse-Kubitza

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

14466 08/11/2014 07:10 AM Aaron Marcuse-Kubitza

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

14454 08/11/2014 03:40 AM Aaron Marcuse-Kubitza

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

14451 08/11/2014 02:16 AM Aaron Marcuse-Kubitza

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

14448 08/10/2014 05:53 AM Aaron Marcuse-Kubitza

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.

14436 08/09/2014 08:46 PM Aaron Marcuse-Kubitza

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

14434 08/09/2014 08:42 PM Aaron Marcuse-Kubitza

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

14433 08/09/2014 08:25 PM Aaron Marcuse-Kubitza

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

14432 08/09/2014 08:11 PM Aaron Marcuse-Kubitza

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

14431 08/09/2014 07:45 PM Aaron Marcuse-Kubitza

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

14430 08/09/2014 07:43 PM Aaron Marcuse-Kubitza

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

14426 08/09/2014 07:19 PM Aaron Marcuse-Kubitza

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

14424 08/09/2014 06:52 PM Aaron Marcuse-Kubitza

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

14423 08/09/2014 06:50 PM Aaron Marcuse-Kubitza

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)

14422 08/09/2014 05:54 AM Aaron Marcuse-Kubitza

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

14421 08/09/2014 05:27 AM Aaron Marcuse-Kubitza

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

14417 08/05/2014 05:31 PM Aaron Marcuse-Kubitza

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

14416 08/04/2014 06:25 AM Aaron Marcuse-Kubitza

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

14414 08/04/2014 06:17 AM Aaron Marcuse-Kubitza

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

14413 08/04/2014 06:10 AM Aaron Marcuse-Kubitza

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

14408 08/02/2014 07:58 PM Aaron Marcuse-Kubitza

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

14388 07/28/2014 11:58 PM Aaron Marcuse-Kubitza

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

14379 07/28/2014 04:45 PM Aaron Marcuse-Kubitza

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

14378 07/28/2014 04:33 PM Aaron Marcuse-Kubitza

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

14377 07/28/2014 04:21 PM Aaron Marcuse-Kubitza

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

14376 07/28/2014 04:02 PM Aaron Marcuse-Kubitza

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

14375 07/28/2014 03:48 PM Aaron Marcuse-Kubitza

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

14368 07/26/2014 10:16 PM Aaron Marcuse-Kubitza

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

14367 07/26/2014 10:15 PM Aaron Marcuse-Kubitza

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.

14366 07/26/2014 09:57 PM Aaron Marcuse-Kubitza

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

14365 07/26/2014 08:58 PM Aaron Marcuse-Kubitza

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

14364 07/26/2014 08:48 PM Aaron Marcuse-Kubitza

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

14363 07/26/2014 08:44 PM Aaron Marcuse-Kubitza

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

14362 07/26/2014 08:38 PM Aaron Marcuse-Kubitza

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

14361 07/26/2014 08:24 PM Aaron Marcuse-Kubitza

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

14360 07/26/2014 08:19 PM Aaron Marcuse-Kubitza

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`

14359 07/26/2014 08:13 PM Aaron Marcuse-Kubitza

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

14358 07/26/2014 07:52 PM Aaron Marcuse-Kubitza

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

14357 07/26/2014 07:43 PM Aaron Marcuse-Kubitza

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

14356 07/26/2014 07:40 PM Aaron Marcuse-Kubitza

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

14347 07/26/2014 05:16 PM Aaron Marcuse-Kubitza

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

14332 07/25/2014 02:21 PM Aaron Marcuse-Kubitza

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

14330 07/25/2014 12:41 PM Aaron Marcuse-Kubitza

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

14329 07/25/2014 12:14 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added derived column "matched~Name[_no_author]___@TNRS__@vegpath.org", which removes the "No suitable matches found." string

14328 07/22/2014 06:50 AM Aaron Marcuse-Kubitza

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

14327 07/22/2014 06:46 AM Aaron Marcuse-Kubitza

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

14326 07/22/2014 06:44 AM Aaron Marcuse-Kubitza

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

14325 07/22/2014 06:41 AM Aaron Marcuse-Kubitza

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

14324 07/22/2014 05:47 AM Aaron Marcuse-Kubitza

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

14323 07/22/2014 05:30 AM Aaron Marcuse-Kubitza

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

14318 07/22/2014 04:12 AM Aaron Marcuse-Kubitza

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

14317 07/22/2014 04:01 AM Aaron Marcuse-Kubitza

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

14313 07/22/2014 03:25 AM Aaron Marcuse-Kubitza

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

14312 07/22/2014 03:23 AM Aaron Marcuse-Kubitza

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

14311 07/22/2014 03:20 AM Aaron Marcuse-Kubitza

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

14310 07/22/2014 03:12 AM Aaron Marcuse-Kubitza

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

14309 07/22/2014 02:44 AM Aaron Marcuse-Kubitza

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

14308 07/22/2014 02:36 AM Aaron Marcuse-Kubitza

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

14307 07/22/2014 02:33 AM Aaron Marcuse-Kubitza

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

14306 07/22/2014 02:27 AM Aaron Marcuse-Kubitza

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

14305 07/22/2014 02:25 AM Aaron Marcuse-Kubitza

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

14304 07/22/2014 01:48 AM Aaron Marcuse-Kubitza

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

14303 07/22/2014 01:37 AM Aaron Marcuse-Kubitza

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

14284 07/21/2014 05:44 PM Aaron Marcuse-Kubitza

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

14283 07/21/2014 05:30 PM Aaron Marcuse-Kubitza

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

14282 07/21/2014 05:26 PM Aaron Marcuse-Kubitza

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

14281 07/21/2014 05:13 PM Aaron Marcuse-Kubitza

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

14279 07/21/2014 04:34 PM Aaron Marcuse-Kubitza

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

14278 07/21/2014 04:25 PM Aaron Marcuse-Kubitza

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

14277 07/21/2014 04:08 PM Aaron Marcuse-Kubitza

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

14275 07/21/2014 03:48 PM Aaron Marcuse-Kubitza

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

14273 07/21/2014 03:34 PM Aaron Marcuse-Kubitza

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

14269 07/21/2014 09:02 AM Aaron Marcuse-Kubitza

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

14268 07/21/2014 08:47 AM Aaron Marcuse-Kubitza

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

14267 07/21/2014 08:44 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added derived columns "[matched_]scientificName[_with_author]__@DwC__@vegpath.org", "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"

14266 07/21/2014 08:29 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added derived columns "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org", "[accepted_]infraspecificEpithet__@DwC__@vegpath.org"

14265 07/21/2014 08:26 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added derived column "__accepted_infraspecific_{rank,epithet}"

14264 07/21/2014 08:19 AM Aaron Marcuse-Kubitza

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

14258 07/21/2014 06:55 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: derived_col_update(): steps to modify: also need to run util.derived_cols_populate()

14257 07/21/2014 06:54 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added derived columns "[accepted_]genus__@DwC__@vegpath.org", "[accepted_]specificEpithet__@DwC__@vegpath.org"

14254 07/21/2014 06:26 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: ran derived_cols_update()

14161 07/19/2014 09:21 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: documented that whenever columns are renamed, util.derived_cols_sync() should be run

14150 07/19/2014 06:54 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match__fill_derived(): updated using new util.derived_cols_sync()

14132 07/19/2014 02:52 AM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: taxon_match: to populate a new column: also need to recluster table so rows are exported in sorted order

14125 07/18/2014 11:40 PM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: taxon_match: cluster the table so the rows are always exported in the same order, even when an UPDATE statement is used to run triggers

14122 07/18/2014 03:18 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added _accepted{genus,specific_epithet} derived column, using the steps at wiki.vegpath.org/Postgres_queries#maintaining-derived-column-formulas-across-column-renames

14111 07/17/2014 04:13 PM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: taxon_match: added back * prefixes on TNRS-namespace column names

14110 07/17/2014 03:34 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon: taxon_best_match: don't alias to `s` since this is no longer a nested select

14109 07/17/2014 03:32 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon: nested select: use just taxon_best_match since this no longer performs renamings

14108 07/17/2014 03:27 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon: renamed output columns to match input columns, so that the nested select would not be performing any renamings

14107 07/17/2014 03:05 PM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: MatchedTaxon: added all columns from taxon_match (some of them apparently hadn't been included in MatchedTaxon)