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# Date Author Comment
13986 07/11/2014 09:46 AM Aaron Marcuse-Kubitza

fix: inputs/VASCAN/Source/map.csv: observationGranularity should not be specimen because this datasource contains only taxa

13975 07/11/2014 07:34 AM Aaron Marcuse-Kubitza

fix: inputs/.geoscrub/geoscrub_output/: added _no_import because these tables are metadata that is used in the analytical DB. this is better than relying on bin/import_all not to import these.

13972 07/10/2014 06:32 PM Aaron Marcuse-Kubitza

fix: inputs/IUCN/: renamed to inputs/.IUCN/ (see issue #940)

13971 07/10/2014 06:04 PM Aaron Marcuse-Kubitza

fix: inputs/newWorld/: renamed to inputs/.newWorld/ (see issue #940)

13970 07/10/2014 04:59 PM Aaron Marcuse-Kubitza

bugfix: inputs/IRMNG/: renamed to inputs/.IRMNG/ so that this comes before TNRS, which depends on it (this is a metadata datasource, so it can start with "."). part of issue #940.

13965 07/10/2014 12:17 PM Aaron Marcuse-Kubitza

inputs/GBIF/_MySQL/.rsync_ignore: don't exclude GBIFPortalDB-*.data.sql.gz, even though this is an intermediate file, because it's better to have a backup of it locally. this was excluded in r13316 (2014-4-24) to free up disk space on the local machine.

13964 07/10/2014 10:57 AM Aaron Marcuse-Kubitza

fix: inputs/Madidi/LocationObservation/postprocess.sql: parse Spanish dates

13947 07/09/2014 02:50 PM Aaron Marcuse-Kubitza

fix: mappings/VegCore-VegBIEN.csv: mapped DwC year/month/day, which are split-date alternatives to eventDate. this fixes the missing eventDate in FIA.

13946 07/09/2014 02:45 PM Aaron Marcuse-Kubitza

bugfix: inputs/FIA/*/VegBIEN.csv: regenerated, replacing these with symlinks to the file used by new-style import

13945 07/09/2014 02:34 PM Aaron Marcuse-Kubitza

inputs/FIA/taxon_observation.**/test.xml.ref: updated

13944 07/09/2014 02:34 PM Aaron Marcuse-Kubitza

inputs/FIA/TREE/test.xml.ref: updated

13943 07/09/2014 02:29 PM Aaron Marcuse-Kubitza

inputs/FIA/REF_RESEARCH_STATION/test.xml.ref: updated

13940 07/09/2014 12:14 PM Aaron Marcuse-Kubitza

fix: inputs/bien2_traits/TraitObservation/map.csv: mapped VisitingDate to eventDate

13939 07/09/2014 12:05 PM Aaron Marcuse-Kubitza

fix: inputs/Madidi/LocationObservation/postprocess.sql: populated missing eventDate from PlotInventoryName (authorEventCode)

13932 07/09/2014 07:03 AM Aaron Marcuse-Kubitza

removed no longer needed inputs/.TNRS/grants.sql, since the grants in schema.sql are now being run

13931 07/09/2014 07:03 AM Aaron Marcuse-Kubitza

bugfix: inputs/input.Makefile: sql/install: schema.sql should not be passed through pg_dump_limit because it contains GRANT statements that need to be run

13883 07/04/2014 11:12 AM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13882 07/04/2014 08:45 AM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13881 07/03/2014 08:13 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: matchedFamily: just use Name_matched_accepted_family, because TNRS has now been reloaded so that the names that were missing this have it populated

13879 07/03/2014 12:34 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: taxon_match__valid_match: replaced with taxon_best_match__valid_match, which also applies taxon_best_match's filters, since taxon_match is now accessed through taxon_best_match

13878 07/03/2014 12:17 AM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: MatchedTaxon: use taxon_best_match instead of taxon_match because this should provide only one match per taxon

13875 06/26/2014 06:30 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added taxon_best_match view

13874 06/26/2014 06:12 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added taxon_match__one_selected_match unique index

13871 06/26/2014 05:41 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match__fill(): split into separate DECLARE blocks for each field for clarity

13870 06/26/2014 04:58 AM Aaron Marcuse-Kubitza

inputs/.TNRS/data.sql: refreshed

13869 06/26/2014 04:57 AM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*

13868 06/26/2014 04:33 AM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*

13867 06/26/2014 04:28 AM Aaron Marcuse-Kubitza

inputs/.TNRS/data.sql: refreshed

13866 06/26/2014 04:11 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: insert names via taxon_match_input auto-updatable view instead of directly into taxon_match, to allow the taxon_match columns to be renamed while still supporting inserts using the TNRS column names

13864 06/26/2014 02:41 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name

13863 06/26/2014 02:39 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name

13861 06/26/2014 02:14 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name

13853 06/25/2014 04:28 PM Aaron Marcuse-Kubitza

inputs/.TNRS/data.sql: refreshed

13852 06/25/2014 04:25 PM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: taxon_name_is_safe(): need to use `NOT (_ = ANY()) instead of ` != ANY`, because the != operator is applied to each element

13851 06/25/2014 03:47 PM Aaron Marcuse-Kubitza

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

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

13846 06/25/2014 10:39 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: `taxon_scrub.scrubbed_unique_taxon_name.*`: added to-modify instructions

13845 06/25/2014 10:36 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: *_modify(): merged these into the "to modify" instructions in the corresponding views, because there is no need to create a separate *_modify() function for every view now that their definitions are all the same

13800 06/18/2014 03:53 PM Aaron Marcuse-Kubitza

schemas/public_.sql, inputs/.TNRS/schema.sql: upgraded to Postgres 9.3.4 format, which removes trailing " "

13763 06/13/2014 05:49 PM Aaron Marcuse-Kubitza

*: use vegbiendev:/home/bien instead of /home/bien/svn

13745 06/13/2014 01:16 PM Aaron Marcuse-Kubitza

merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema

13744 06/13/2014 01:03 PM Aaron Marcuse-Kubitza

removed no longer needed inputs/VegBIEN/fs symlink. use web/.fs instead.

13686 06/06/2014 06:47 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: unsafe_taxon_names(): removed the name with "spp." now that this TNRS bug (https://pods.iplantcollaborative.org/jira/browse/TNRS-193) has been fixed

13660 06/05/2014 01:17 PM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13659 06/05/2014 01:17 PM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13658 06/05/2014 12:27 PM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13657 06/05/2014 12:12 PM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13647 06/05/2014 07:24 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()

13646 06/05/2014 07:21 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()

13632 06/05/2014 03:39 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added taxon_name_is_safe()

13631 06/05/2014 03:30 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added unsafe_taxon_names()

13623 06/04/2014 02:09 AM Aaron Marcuse-Kubitza

bugfix: **/.htaccess: redirects with fragment: qsappend does not support fragment, so append it separately

13621 06/04/2014 01:53 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/.htaccess: qsappend does not support fragment, so append it separately

13609 06/03/2014 10:36 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields

13607 06/03/2014 10:21 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this

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).

13589 06/02/2014 04:27 AM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: added back index on Name_submitted, which is needed for tnrs_input_name to work properly (now that there is no automatic index created by a unique constraint)

13587 06/02/2014 03:43 AM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: tnrs: removed unique constraint on Name_submitted, Name_matched because there can be more than one match with the same Name_matched (but different accepted names, etc.)

13586 06/01/2014 09:00 PM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: tnrs.tnrs__valid_match index: made it non-unique to allow multiple matches per name, as is needed to implement #917

13585 06/01/2014 05:00 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: tnrs__match_num__fill(): only fill if not set, to support case where tnrs is being restored from a .sql file (where match_num is already set)

13584 06/01/2014 04:36 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented runtime to add a constraint (3 min)

13583 06/01/2014 04:35 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: unique constraint on Name_submitted: added Name_matched to allow multiple matches per name, as is needed to implement #917

13582 06/01/2014 03:44 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented how to populate a new column

13581 06/01/2014 03:41 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: pkey: use match_num instead of Name_number to allow multiple matches per name, as is needed to implement #917

13580 05/31/2014 10:31 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs.match_num: made it NOT NULL now that it's populated

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

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

13578 05/31/2014 10:25 PM Aaron Marcuse-Kubitza

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

13577 05/31/2014 09:50 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented how to add and remove columns

13575 05/31/2014 08:58 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line

13574 05/31/2014 08:11 PM Aaron Marcuse-Kubitza

inputs/test_taxonomic_names/_scrub/*: updated to TNRS schema

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

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

13572 05/31/2014 08:06 PM Aaron Marcuse-Kubitza

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

13570 05/31/2014 06:44 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added tnrs__match_num__next()

13567 05/30/2014 06:34 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)

13540 05/27/2014 10:13 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_scrub.scrubbed_unique_taxon_name.*: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)

13533 05/27/2014 12:28 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*

13532 05/27/2014 12:13 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*

13531 05/26/2014 11:54 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_scrub: documented how to modify it

13528 05/26/2014 11:20 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added taxon_scrub_modify()

13527 05/23/2014 06:17 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon_modify(): use simpler util.recreate_view()

13526 05/23/2014 06:15 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon_modify(): documented usage

13518 05/21/2014 07:30 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon_modify(): removed no longer needed DROP VIEW statement

13512 05/21/2014 05:50 PM Aaron Marcuse-Kubitza

fix: schemas/util.sql: force_recreate(): renamed to just recreate(), because "force" normally implies that things will be deleted, which this function does not do

13508 05/21/2014 04:25 PM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: MatchedTaxon.taxonomicStatus: filter using map_taxonomic_status() so that the corrected value is available in the normalized DB, not just analytical_stem

13507 05/21/2014 04:05 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon: to modify: use new MatchedTaxon_modify(), which eliminates the work of putting together the dependent views

13506 05/21/2014 03:53 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added MatchedTaxon_modify()

13503 05/21/2014 04:13 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: map_taxonomic_status(): need to use accepted name instead of scrubbed name (which also includes no-opinion names), as described at http://wiki.vegpath.org/2013-11-14_conference_call#taxonomic-fields. this used to be the accepted name, but got switched when the concatenated name was also used to store the matched name for no-opinion names.

13501 05/21/2014 01:27 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon: documented how to modify it (using util.force_recreate())

13498 05/20/2014 05:46 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon, etc.: added accepted_morphospecies_binomial derived field

13444 05/13/2014 04:50 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: MatchedTaxon.Accepted_name_species: mapped to accepted_species_binomial

13443 05/13/2014 04:09 AM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: COMMENTs: always include newline before and after

13441 05/13/2014 03:46 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: undid rename of accepted name columns to scrubbed_* (r13435), because these are actually not the same (scrubbed_* is the combination of accepted and no-opinion names). the accepted name columns will now be named accepted_*, following the standard naming scheme.

13439 05/13/2014 03:13 AM Aaron Marcuse-Kubitza

fix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: scrubbed_*: use columns from MatchedTaxon whenever possible, to as much as possible avoid the need to join to taxon_scrub.scrubbed_unique_taxon_name.*

13437 05/13/2014 02:29 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/grants.sql: added GRANT statements from schema.sql because these aren't run by `make inputs/.TNRS/reinstall`

13418 05/07/2014 07:17 PM Aaron Marcuse-Kubitza

bugfix: inputs/input.Makefile: $(datasrc_schema_exists): need to use $(datasrc), not $(schema), as $schema is only what this var is called in the runscripts

13417 05/07/2014 06:48 PM Aaron Marcuse-Kubitza

bugfix: inputs/analytical_db/: need dummy table.run file to cause a schema to be created for this datasource

13416 05/07/2014 06:44 PM Aaron Marcuse-Kubitza

fix: inputs/input.Makefile: $(sortFile): don't print the "add any missing tables to $(sortFile)" message every time the Makefile is run

13415 05/07/2014 06:44 PM Aaron Marcuse-Kubitza

bugfix: inputs/input.Makefile: install: only run this for datasource dirs

13414 05/07/2014 05:18 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: install: use ./run's install target for clarity