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From 07/21/2014 to 08/19/2014

08/19/2014

05:13 PM Revision 14528: fix: schemas/util.sql: contained_within_approx(point geocoord, region postgis.geography): use util.geography() instead of implicit cast to suppress "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" NOTICEs
Aaron Marcuse-Kubitza
05:10 PM Revision 14527: schemas/util.sql: added geography(util.geocoord), which suppresses "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" NOTICEs
Aaron Marcuse-Kubitza
04:48 PM Revision 14526: exports/native_status_resolver.csv.run: updated export_() runtime (5 min, now that we're using the narrower New World criterion)
Aaron Marcuse-Kubitza
04:39 PM Revision 14525: fix: schemas/public_.sql: native_status_resolver: don't include rows with New World coordinates that don't also have New World country names, since the NSR only uses the country name
Aaron Marcuse-Kubitza
04:26 PM Revision 14524: schemas/public_.sql: native_status_resolver: removed rows with is_geovalid NULL, at Brad's request. note that this removes valid rows with standardized country names.
Aaron Marcuse-Kubitza
04:01 PM Revision 14523: exports/native_status_resolver.csv.run: updated export_() runtime (30 min)
Aaron Marcuse-Kubitza
03:28 PM Revision 14522: fix: schemas/public_.sql: native_status_resolver: added country IS NOT NULL filter requested by Brad
Aaron Marcuse-Kubitza
02:35 PM Revision 14521: fix: schemas/public_.sql: native_status_resolver: remove the id because this prevents SELECT DISTINCT from having the desired effect. instead, the results will be joined back using the other columns.
Aaron Marcuse-Kubitza
02:25 PM Revision 14520: exports/native_status_resolver.csv.run: upload_(): documented runtime (2.5 min)
Aaron Marcuse-Kubitza
02:18 PM Revision 14519: bugfix: exports/native_status_resolver.csv.run: upload_(): $live must be exported
Aaron Marcuse-Kubitza
02:15 PM Revision 14518: exports/native_status_resolver.csv.run: upload_(): use `live=1` instead for consistency with other invocations of put
Aaron Marcuse-Kubitza
02:14 PM Revision 14517: fix: exports/native_status_resolver.csv.run: upload_(): need `l=1`
Aaron Marcuse-Kubitza
02:12 PM Revision 14516: exports/native_status_resolver.csv.run: documented export_() runtime (45 min)
Aaron Marcuse-Kubitza
01:48 PM Revision 14515: exports/native_status_resolver.csv.run: added upload_() to get the file onto nimoy
Aaron Marcuse-Kubitza
01:25 PM Revision 14514: added exports/native_status_resolver.csv.run
Aaron Marcuse-Kubitza
01:23 PM Revision 14513: schemas/public_.sql: added native_status_resolver view, requested by Brad (wiki.vegpath.org/Data_requests)
Aaron Marcuse-Kubitza
11:47 AM Revision 14512: inputs/publishable datasources.xlsx: udpated
Aaron Marcuse-Kubitza
11:20 AM Task #946 (New): update the column names in the VegBIEN example queries to reflect Brian M's renamings
* the VegBIEN example queries are at *[[VegBIEN FAQ#asked-by-Brian-E-on-2014-8-8]] > asked by Brian E on 2014-8-8*
*...
Aaron Marcuse-Kubitza
08:37 AM Revision 14511: lib/tnrs.py: documentation about output of the retrieve step: added that this is also unusable because the array does not contain all the columns and contains no column names
Aaron Marcuse-Kubitza
07:54 AM Revision 14510: removed no longer used web/BIEN3/Redmine/main/. use Redmine/!__ instead.
Aaron Marcuse-Kubitza
07:52 AM Revision 14509: web/BIEN3/Redmine/issues/.htaccess: perform .. redirects using new ! prefix
Aaron Marcuse-Kubitza
07:51 AM Revision 14508: web/BIEN3/Redmine/.htaccess: enable redirects that avoid using a subdir's .htaccess
Aaron Marcuse-Kubitza
07:46 AM Revision 14507: web/BIEN3/Redmine/wiki/.htaccess: removed no longer needed ignore_fs, since the .htaccess does not have RewriteRules that would need this in a RewriteCond
Aaron Marcuse-Kubitza
07:42 AM Revision 14506: web/BIEN3/Redmine/issues/.htaccess: main issues page: added default filter conditions
Aaron Marcuse-Kubitza
07:41 AM Revision 14505: bugfix: web/BIEN3/Redmine/issues/.htaccess: need to redirect to separate URL for individual issues, because they are not located under the issues/ subdir in Redmine
Aaron Marcuse-Kubitza
06:35 AM Revision 14504: added web/.issues symlink and dest dir (needed because Apache does not support dangling symlinks)
Aaron Marcuse-Kubitza
06:35 AM Revision 14503: web/BIEN3/Redmine/wiki/.htaccess: documented that this dir is needed because Apache does not support dangling symlinks
Aaron Marcuse-Kubitza
06:32 AM Revision 14502: bugfix: web/.htaccess: need to expand top-level symlinks to avoid RewriteBase issues
Aaron Marcuse-Kubitza
06:29 AM Revision 14501: web/main.conf: added RewriteMap for readlink
Aaron Marcuse-Kubitza
06:28 AM Revision 14500: added web/readlink
Aaron Marcuse-Kubitza
05:52 AM Revision 14499: web/links/index.htm: updated to Firefox bookmarks: updated favicons
Aaron Marcuse-Kubitza
05:47 AM Revision 14498: web/links/index.htm: updated to Firefox bookmarks: updated favicons
Aaron Marcuse-Kubitza

08/18/2014

04:52 PM Revision 14497: web/BIEN3/Redmine/wiki/.htaccess: just use this dir as symlink dest, since the dir name is the same as the URL path within Redmine
Aaron Marcuse-Kubitza
04:50 PM Revision 14496: web/.htaccess: don't rewrite existing files/dirs: allow forcing rewrite of existing things with %{ENV:ignore_fs}
Aaron Marcuse-Kubitza
03:41 PM Revision 14495: web/BIEN3/Redmine/svn-web/.htaccess: use Redmine/ instead of main/ subdir
Aaron Marcuse-Kubitza
03:37 PM Revision 14494: web/BIEN3/Redmine/.htaccess: point this to the Redmine root instead of to the wiki, to avoid the need to append /main
Aaron Marcuse-Kubitza
03:21 PM Revision 14493: backups/vegbien.r14089.backup.md5: updated
Aaron Marcuse-Kubitza
01:58 PM Revision 14492: 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)
Aaron Marcuse-Kubitza
10:01 AM Bug #945 (New): incorrect synonym being selected in TNRS
_this is "TNRS-195":https://pods.iplantcollaborative.org/jira/browse/TNRS-195 on the TNRS JIRA bug tracker_
TNRS's...
Aaron Marcuse-Kubitza

08/17/2014

12:04 PM Revision 14491: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
07:49 AM Revision 14490: 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)
Aaron Marcuse-Kubitza
07:23 AM Revision 14489: schemas/util.sql: added date_part_fix()
Aaron Marcuse-Kubitza

08/16/2014

05:55 PM Revision 14488: schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.
Aaron Marcuse-Kubitza
05:51 PM Revision 14487: schemas/public_.sql: added view_full_occurrence_individual_*GBIF, analytical_stem_*GBIF requested by Mark. note that this change has already been made on vegbiendev.
Aaron Marcuse-Kubitza
05:37 PM Revision 14486: schemas/VegBIEN/data_dictionary/VegBIEN data dictionary.xlsx: updated
Aaron Marcuse-Kubitza
05:15 PM Revision 14485: schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.
Aaron Marcuse-Kubitza
05:11 PM Revision 14484: schemas/public_.sql: view_full_occurrence_individual, analytical_stem: renamed columns to shortened names at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.
Aaron Marcuse-Kubitza
02:58 PM Revision 14483: schemas/public_.sql: analytical_stem_view: renamed to analytical_stem since this replaces the materialized analytical_stem table. note that this change has already been made on vegbiendev.
Aaron Marcuse-Kubitza
02:35 PM Revision 14482: schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.
Aaron Marcuse-Kubitza
01:20 PM Revision 14481: schemas/public_.sql: viewFullOccurrence_individual: re-ran viewFullOccurrence_individual_view_modify() to udpate this
Aaron Marcuse-Kubitza
01:15 PM Revision 14480: bugfix: schemas/util.sql: copy_struct(): also need to util.copy_comment() because CREATE TABLE __ INCLUDING ALL is missing this
Aaron Marcuse-Kubitza
01:11 PM Revision 14479: schemas/util.sql: added copy_comment(regclass, regclass)
Aaron Marcuse-Kubitza
12:29 PM Revision 14478: schemas/public_.sql: viewFullOccurrence_individual_view: CREATE INDEX runtime: documented 2-column runtime (~2 h)
Aaron Marcuse-Kubitza
12:06 PM Revision 14477: exports/analytical_stem_*GBIF.csv.run: documented runtime (40 min-1.2 h)
Aaron Marcuse-Kubitza
09:36 AM Revision 14476: exports/view_full_occurrence_individual_*GBIF.csv.run: documented runtime (20-30 min)
Aaron Marcuse-Kubitza
08:37 AM Revision 14475: added exports/analytical_stem_GBIF.csv.run, analytical_stem_non_GBIF.csv.run
Aaron Marcuse-Kubitza

08/15/2014

07:15 PM Revision 14474: added exports/view_full_occurrence_individual_GBIF.csv.run, view_full_occurrence_individual_non_GBIF.csv.run
Aaron Marcuse-Kubitza
04:13 PM Revision 14473: schemas/public_.sql: viewFullOccurrence_individual_view: added "after updating this" instructions
Aaron Marcuse-Kubitza
04:01 PM Revision 14472: schemas/public_.sql: viewFullOccurrence_individual_view: documented CREATE INDEX runtime (10 min - 1.5 h depending on the datatype and % populated)
Aaron Marcuse-Kubitza
03:32 PM Revision 14471: web/links/index.htm: updated to Firefox bookmarks: updated to use frenzy instead of starscream
Aaron Marcuse-Kubitza

08/14/2014

03:25 PM Revision 14470: fix: lib/tnrs.py: retrieval_request_template: source_sorting (Constrain by Source): corrected explanation to reflect that the behavior is actually the same in both modes, since only one match is ever marked as selected, and that match should always come first
Aaron Marcuse-Kubitza
03:03 PM Bug #943: in TNRS, the Constrain by Source option is applied incorrectly to the results download
there is now a much faster workaround, described in the last paragraph of the issue description Aaron Marcuse-Kubitza
10:50 AM Revision 14469: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza

08/11/2014

08:53 AM Bug #944 (New): fix phpPgAdmin bug that crashes the DB when browsing large tables
use "@provider_count@":http://vegbiendev.nceas.ucsb.edu/VegBIEN/public/provider_count/:display to test this Aaron Marcuse-Kubitza
07:48 AM Revision 14468: inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_name index
Aaron Marcuse-Kubitza
07:46 AM Revision 14467: inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_family index
Aaron Marcuse-Kubitza
07:10 AM Revision 14466: inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_species_binomial index
Aaron Marcuse-Kubitza
05:28 AM Revision 14465: bugfix: schemas/public_.sql: *_view_modify(): need to set the search_path so that tables are created in the same schema as the function, rather than whichever schema happens to be at the beginning of the search_path
Aaron Marcuse-Kubitza
05:19 AM Revision 14464: bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to support being used directly instead of via a materialized table
Aaron Marcuse-Kubitza
05:13 AM Revision 14463: schemas/public_.sql: removed no longer used analytical_stem. use analytical_stem_view or viewFullOccurrence_individual instead.
Aaron Marcuse-Kubitza
05:08 AM Revision 14462: fix: schemas/public_.sql: viewfulloccurrence_individual_view_modify(): fixed capitalization in function name (needs "" to preserve case)
Aaron Marcuse-Kubitza
05:03 AM Revision 14461: schemas/public_.sql: other derived views: use viewFullOccurrence_individual instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)
Aaron Marcuse-Kubitza
05:01 AM Revision 14460: schemas/public_.sql: validation views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)
Aaron Marcuse-Kubitza
04:57 AM Revision 14459: schemas/public_.sql: derived views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)
Aaron Marcuse-Kubitza
04:46 AM Revision 14458: bugfix: schemas/util.sql: expansion_min_cols(): increased to properly handle all public-schema views (the largest is currently 2014-6-12.Jeff_Ott.climatic_range_determinants)
Aaron Marcuse-Kubitza
04:35 AM Revision 14457: schemas/util.sql: view_def_to_orig(): use new expansion_min_cols() for easier configuration
Aaron Marcuse-Kubitza
04:33 AM Revision 14456: schemas/util.sql: added expansion_min_cols() (the minimum # of cols from the same table to be treated as a * expression)
Aaron Marcuse-Kubitza
04:05 AM Revision 14455: fix: schemas/public_.sql: analytical_stem_view: regenerated columns list for viewFullOccurrence_individual (instead of viewFullOccurrence_individual_view)
Aaron Marcuse-Kubitza
03:40 AM Revision 14454: bugfix: mappings/VegCore-VegBIEN.csv: prefixed taxonomic ranks: use _concat_nullify() so that the prefix is only added if the epithet is non-NULL
Aaron Marcuse-Kubitza
03:29 AM Revision 14453: fix: schemas/util.sql: col_re(): support column names with " in them
Aaron Marcuse-Kubitza
02:59 AM Revision 14452: schemas/util.sql: added _concat_nullify(), which uses || instead of concat()
Aaron Marcuse-Kubitza
02:16 AM Revision 14451: bugfix: inputs/FIA/REF_RESEARCH_STATION/map.csv: mapped country, which is not provided in the FIA data
Aaron Marcuse-Kubitza
01:46 AM Revision 14450: schemas/public_.sql: removed no longer used threatened_taxonlabel_view. use iucn_red_list_view instead.
Aaron Marcuse-Kubitza
01:35 AM Revision 14449: schemas/public_.sql: viewFullOccurrence_individual_view: documented materialize time (22 h)
Aaron Marcuse-Kubitza

08/10/2014

05:53 AM Revision 14448: 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.
Aaron Marcuse-Kubitza
05:28 AM Revision 14447: /README.TXT: Full database import: added steps to re-run geoscrubbing
Aaron Marcuse-Kubitza
05:22 AM Revision 14446: exports/geoscrub_input.csv.run: export_(): updated runtime (30 s)
Aaron Marcuse-Kubitza
03:57 AM Revision 14445: fix: exports/viewFullOccurrence_*.csv.run: need to limit # rows to 5000 as requested by Bob
Aaron Marcuse-Kubitza
03:42 AM Revision 14444: schemas/public_.sql: viewFullOccurrence_*: documented materialize time
Aaron Marcuse-Kubitza

08/09/2014

10:23 PM Revision 14443: bin/make_analytical_db: materialize viewFullOccurrence_individual_view instead of analytical_stem_view because analytical_stem_view is now generatable via a simple join onto viewFullOccurrence_individual_view. this avoids running into potential disk space constraints when materializing and backing up both tables (~50 GB/table * 2 tables * 2 copies (incl. the backup) = 200 GB, which is very close to the available disk space).
Aaron Marcuse-Kubitza
10:17 PM Revision 14442: schemas/public_.sql: analytical_stem_view: use new materialized viewFullOccurrence_individual
Aaron Marcuse-Kubitza
10:08 PM Revision 14441: schemas/public_.sql: added viewFullOccurrence_individual by running viewFullOccurrence_individual_view_modify()
Aaron Marcuse-Kubitza
10:05 PM Revision 14440: schemas/public_.sql: added viewFullOccurrence_individual_view_modify(), analogous to analytical_stem_view_modify()
Aaron Marcuse-Kubitza
09:52 PM Revision 14439: bin/make_analytical_db: removed extra () around psql_verbose_vegbien
Aaron Marcuse-Kubitza
09:51 PM Revision 14438: bin/make_analytical_db: removed no longer used mk_table()
Aaron Marcuse-Kubitza
09:49 PM Revision 14437: bin/make_analytical_db: use more up-to-date *_view_modify() functions instead of mk_table()
Aaron Marcuse-Kubitza
08:46 PM Revision 14436: inputs/.TNRS/schema.sql: removed no longer used view ValidMatchedTaxon. use taxon_scrub instead.
Aaron Marcuse-Kubitza
08:44 PM Revision 14435: schemas/public_.sql: iucn_red_list_view: use taxon_scrub instead of ValidMatchedTaxon since they are equivalent
Aaron Marcuse-Kubitza
08:42 PM Revision 14434: inputs/.TNRS/schema.sql: taxon_scrub: use taxon_best_match directly, to avoid the need for a separate ValidMatchedTaxon view
Aaron Marcuse-Kubitza
08:25 PM Revision 14433: fix: inputs/.TNRS/schema.sql: taxon_scrub: merged synonymous columns
Aaron Marcuse-Kubitza
08:11 PM Revision 14432: schemas/vegbien.sql: taxon_scrub: documented steps to merge synonymous columns
Aaron Marcuse-Kubitza
07:45 PM Revision 14431: inputs/.TNRS/schema.sql: removed no longer used view MatchedTaxon. use taxon_best_match instead.
Aaron Marcuse-Kubitza
07:43 PM Revision 14430: inputs/.TNRS/schema.sql: ValidMatchedTaxon: use taxon_best_match now that it's equivalent to MatchedTaxon
Aaron Marcuse-Kubitza
07:38 PM Revision 14429: bugfix: schemas/public_.sql: tnrs_input_name: use taxon_match instead of taxon_best_match because there is no index on taxon_match that includes just the filters used by taxon_best_match
Aaron Marcuse-Kubitza
07:37 PM Revision 14428: schemas/public_.sql: tnrs_input_name: use taxon_best_match now that it's equivalent to MatchedTaxon
Aaron Marcuse-Kubitza
07:20 PM Revision 14427: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
07:19 PM Revision 14426: fix: inputs/.TNRS/schema.sql: MatchedTaxon: merged synonymous columns
Aaron Marcuse-Kubitza
07:02 PM Revision 14425: fix: schemas/util.sql: view_is_subset_or_renaming(): views with CASE statements are also not subsets/renamings
Aaron Marcuse-Kubitza
06:52 PM Revision 14424: inputs/.TNRS/schema.sql: removed no longer used taxon_scrub.scrubbed_unique_taxon_name.* . use taxon_scrub instead.
Aaron Marcuse-Kubitza
06:50 PM Revision 14423: 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)
Aaron Marcuse-Kubitza
05:54 AM Revision 14422: inputs/.TNRS/schema.sql: MatchedTaxon: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.
Aaron Marcuse-Kubitza
05:27 AM Revision 14421: inputs/.TNRS/schema.sql: taxon_scrub: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.
Aaron Marcuse-Kubitza

08/08/2014

07:14 PM Revision 14420: added exports/viewFullOccurrence_{CVS,VegBank,NCU}.csv.run
Aaron Marcuse-Kubitza
07:13 PM Revision 14419: schemas/public_.sql: added viewFullOccurrence_{CVS,VegBank,NCU} for Bob
Aaron Marcuse-Kubitza
02:32 PM Revision 14418: bugfix: schemas/util.sql: added GRANT USAGE for bien_read, public_ so that util schema functions can be called by other users
Aaron Marcuse-Kubitza

08/05/2014

05:31 PM Revision 14417: inputs/.TNRS/schema.sql: taxon_match: to port derived column changes to vegbiendev: derived_cols_export() code: documented runtime (6 h)
Aaron Marcuse-Kubitza

08/04/2014

06:25 AM Revision 14416: bugfix: inputs/.TNRS/schema.sql: removed no longer used derived column __accepted_infraspecific_label, which had a buggy formula that broke derived_cols_populate()
Aaron Marcuse-Kubitza
06:18 AM Revision 14415: bugfix: schemas/util.sql: drop_derived_col(): also need to run util.derived_cols_trigger_update()
Aaron Marcuse-Kubitza
06:17 AM Revision 14414: bugfix: inputs/.TNRS/schema.sql: removed no longer used derived column __accepted_infraspecific_label, which had a buggy formula that broke derived_cols_populate()
Aaron Marcuse-Kubitza
06:10 AM Revision 14413: fix: inputs/.TNRS/schema.sql: taxon_match: to remove a column: updated instructions
Aaron Marcuse-Kubitza
05:09 AM Revision 14412: bugfix: lib/sh/util.sh: str2varname(): need to lowercase str because on case-insensitive filesystems, paths sometimes canonicalize to a different capitalization than the original
Aaron Marcuse-Kubitza
05:00 AM Revision 14411: lib/sh/util.sh: added lowercase()
Aaron Marcuse-Kubitza

08/03/2014

09:54 PM Revision 14410: bugfix: lib/sh/util.sh: die(): need stub since this is invoked before it's defined
Aaron Marcuse-Kubitza
09:12 PM Revision 14409: bugfix: lib/sh/util.sh: setup_log_fd(): don't change $log_fd to stdlog until stdlog is set up, to avoid "Bad file descriptor" errors
Aaron Marcuse-Kubitza

08/02/2014

07:58 PM Revision 14408: **: updated to use the local machine's new hostname, frenzy
Aaron Marcuse-Kubitza
07:13 PM Revision 14407: lib/sh/util.sh: func_override(), copy_func(): added echo_func to facilitate debugging
Aaron Marcuse-Kubitza
07:12 PM Revision 14406: bugfix: lib/sh/util.sh: stubs: log++ alias also needs to be moved to stub section
Aaron Marcuse-Kubitza

08/01/2014

06:31 PM Revision 14405: bugfix: lib/Firefox_bookmarks.reformat.csv: URLs: match only the uppercase tags used by Firefox, not any lowercase tags added by the user
Aaron Marcuse-Kubitza
05:42 PM Revision 14404: fix: lib/Firefox_bookmarks.reformat.csv: page's self-description: updated comment to match regexp
Aaron Marcuse-Kubitza
05:39 PM Revision 14403: bugfix: lib/Firefox_bookmarks.reformat.csv: page's self-description: updated "page's self-description: " prefix to remove
Aaron Marcuse-Kubitza
04:50 PM Revision 14402: web/links/index.htm: updated to Firefox bookmarks: added links for SSD vs. HDD reliability
Aaron Marcuse-Kubitza
04:22 PM Revision 14401: /README.TXT: added steps to restore from Time Machine
Aaron Marcuse-Kubitza
04:15 PM Revision 14400: /README.TXT: added steps to back up the local machine's hard drive
Aaron Marcuse-Kubitza
04:13 PM Revision 14399: /README.TXT: to synchronize a Mac's settings with my testing machine's: renamed to "to back up the local machine's settings"
Aaron Marcuse-Kubitza
04:11 PM Revision 14398: /README.TXT: to synchronize a Mac's settings with my testing machine's: removed download section because we don't use this
Aaron Marcuse-Kubitza
06:01 AM Revision 14397: added backups/vegbien.r14089.backup.md5
Aaron Marcuse-Kubitza
06:01 AM Revision 14396: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
05:47 AM Revision 14395: bin/after_import: use new bin/make_backups
Aaron Marcuse-Kubitza
05:47 AM Revision 14394: bugfix: bin/make_backups: need to `popd` when done
Aaron Marcuse-Kubitza
05:46 AM Revision 14393: bugfix: bin/make_backups: need to `set +x` when done
Aaron Marcuse-Kubitza
05:44 AM Revision 14392: bin/make_backups: run with initial "." so background processes will be owned by the invoking shell
Aaron Marcuse-Kubitza
04:40 AM Revision 14391: added bin/make_backups
Aaron Marcuse-Kubitza
01:59 AM Revision 14390: web/links/index.htm: updated to Firefox bookmarks: VirtualBox: performance: added that context-switching also imposes an overhead, in addition to sandboxing.
Aaron Marcuse-Kubitza
01:16 AM Revision 14389: web/links/index.htm: updated to Firefox bookmarks: BIEN: added list of machines this has been tested on. VirtualBox: added links to performance considerations of running in a VM.
Aaron Marcuse-Kubitza

07/28/2014

11:58 PM Revision 14388: inputs/.TNRS/schema.sql: added new derived columns to derived views
Aaron Marcuse-Kubitza
11:58 PM Revision 14387: fix: schemas/util.sql: view_def_to_orig(): need to support aliased columns (produced when a column is renamed)
Aaron Marcuse-Kubitza
05:59 PM Revision 14386: schemas/util.sql: added aliased_col_re()
Aaron Marcuse-Kubitza
05:57 PM Revision 14385: schemas/util.sql: added alias_re()
Aaron Marcuse-Kubitza
05:50 PM Revision 14384: fix: schemas/util.sql: view_is_subset(): renamed to view_is_subset_or_renaming() because this also supports views that just rename columns, which should not be .*-ed by view_def_to_orig()
Aaron Marcuse-Kubitza
05:33 PM Revision 14383: fix: schemas/util.sql: view_def_to_orig(): can't use FROM to alias util.col_re() because that prevents inlining the function
Aaron Marcuse-Kubitza
05:31 PM Revision 14382: fix: schemas/util.sql: view_def_to_orig(): can't use FROM to alias util.col_re() because that prevents inlining the function
Aaron Marcuse-Kubitza
05:24 PM Revision 14381: schemas/util.sql: view_def_to_orig(): use util.col_re() for clarity
Aaron Marcuse-Kubitza
05:20 PM Revision 14380: schemas/util.sql: added col_re()
Aaron Marcuse-Kubitza
04:45 PM Revision 14379: fix: schemas/util.sql: derived_col_update(): also need steps to drop column, because DROP __ CASCADE doesn't work when there are dependent views
Aaron Marcuse-Kubitza
04:33 PM Revision 14378: 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
Aaron Marcuse-Kubitza
04:21 PM Revision 14377: 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
Aaron Marcuse-Kubitza
04:02 PM Revision 14376: 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
Aaron Marcuse-Kubitza
03:48 PM Revision 14375: 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
Aaron Marcuse-Kubitza
03:20 PM Revision 14374: backups/README.TXT: added backup retention policy
Aaron Marcuse-Kubitza

07/27/2014

03:19 PM Revision 14373: bugfix: schemas/util.sql: derived_cols_export(): also need to first run util.derived_cols_remove() if changing the derived column order
Aaron Marcuse-Kubitza
03:15 PM Revision 14372: schemas/util.sql: added derived_cols_remove(), which allows derived columns to be re-created in a different order
Aaron Marcuse-Kubitza
03:01 PM Revision 14371: schemas/util.sql: added drop_derived_col(), which ensures that drop_column() only cascades to views
Aaron Marcuse-Kubitza
02:54 PM Revision 14370: fix: schemas/util.sql: drop_column(): also need to recreate dependent views
Aaron Marcuse-Kubitza
02:26 PM Revision 14369: schemas/util.sql: added drop_constraint()
Aaron Marcuse-Kubitza

07/26/2014

10:16 PM Revision 14368: inputs/.TNRS/schema.sql: taxon_match: `inputs/.TNRS/data.sql.run refresh`: documented runtime (1 min)
Aaron Marcuse-Kubitza
10:15 PM Revision 14367: 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.
Aaron Marcuse-Kubitza
09:57 PM Revision 14366: fix: inputs/.TNRS/schema.sql: taxon_match: added derived column "Accepted_species[_binomial]__@TNRS__@vegpath.org", which removes trailing whitespace
Aaron Marcuse-Kubitza
08:58 PM Revision 14365: inputs/.TNRS/schema.sql: added steps to remove a column and to add a non-derived column
Aaron Marcuse-Kubitza
08:48 PM Revision 14364: inputs/.TNRS/schema.sql: taxon_match: to remove columns or add columns at the end: merged into "to add a new derived column"
Aaron Marcuse-Kubitza
08:44 PM Revision 14363: inputs/.TNRS/schema.sql: to add columns in the middle: renamed to "to move a column to the middle" for clarity
Aaron Marcuse-Kubitza
08:38 PM Revision 14362: inputs/.TNRS/schema.sql: to populate a new column: updated to use util.derived_col_update()
Aaron Marcuse-Kubitza
08:24 PM Revision 14361: fix: inputs/.TNRS/schema.sql: taxon_match: to remove columns or add columns: also need to run util.recreate_view()
Aaron Marcuse-Kubitza
08:19 PM Revision 14360: 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`
Aaron Marcuse-Kubitza
08:13 PM Revision 14359: inputs/.TNRS/schema.sql: added new derived columns to derived views
Aaron Marcuse-Kubitza
07:52 PM Revision 14358: schemas/util.sql: remove_prefix(), remove_suffix(): support case-insensitive matching
Aaron Marcuse-Kubitza
07:43 PM Revision 14357: 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
Aaron Marcuse-Kubitza
07:40 PM Revision 14356: schemas/util.sql: remove_prefix(), remove_suffix(): support case-insensitive matching
Aaron Marcuse-Kubitza
06:54 PM Revision 14355: schemas/util.sql: remove_prefix(), remove_suffix(): support case-insensitive matching
Aaron Marcuse-Kubitza
06:52 PM Revision 14354: schemas/util.sql: added case-sensitive-optional versions of starts_with(), ends_with()
Aaron Marcuse-Kubitza
06:50 PM Revision 14353: schemas/util.sql: added canon_case(str text, case_sensitive boolean)
Aaron Marcuse-Kubitza
06:36 PM Revision 14352: schemas/util.sql: check_constraint_disable(): documented that we can't use ADD CONSTRAINT NOT VALID for this because it does not disable the constraint completely, but instead causes new rows to be validated against it. the ADD CONSTRAINT NOT VALID behavior does not work for the derived columns use case of this function.
Aaron Marcuse-Kubitza
06:17 PM Revision 14351: schemas/public_.sql: *_view_modify(): added repopulate param, which is passed to rematerialize_view()
Aaron Marcuse-Kubitza
06:14 PM Revision 14350: schemas/util.sql: rematerialize_view(): support updating just the table's schema, without populating it
Aaron Marcuse-Kubitza
05:37 PM Revision 14349: schemas/util.sql: rematerialize_view(): don't need extra eval() around table_mod_sql because recreate() performs eval()
Aaron Marcuse-Kubitza
05:28 PM Revision 14348: lib/sh/sync.sh: db_snapshot(): before backing up, trim bloated temp files (eg. from rolled back changes)
Aaron Marcuse-Kubitza
05:16 PM Revision 14347: 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
Aaron Marcuse-Kubitza
04:32 PM Revision 14346: schemas/public_.sql: *_view_modify(): use util.rematerialize_view(), which now supports table mods
Aaron Marcuse-Kubitza
03:47 PM Revision 14345: schemas/util.sql: rematerialize_view(): added support for table mods to run after creating table
Aaron Marcuse-Kubitza
04:53 AM Revision 14344: bugfix: schemas/util.sql: rematerialize_view(): don't populate unless recreate() can successfully recreate the dependent views, to avoid populating the entire table (which for some views can take hours) only to have the changes rolled back by a failing dependent view
Aaron Marcuse-Kubitza
04:42 AM Revision 14343: schemas/util.sql: removed no longer used materialize_view(). use util.copy() instead.
Aaron Marcuse-Kubitza
04:41 AM Revision 14342: schemas/util.sql: rematerialize_view(): call util.copy() directly instead of via util.materialize_view()
Aaron Marcuse-Kubitza
04:35 AM Revision 14341: schemas/util.sql: removed no longer used copy_types_and_data(). use util.materialize_view() instead.
Aaron Marcuse-Kubitza
04:20 AM Revision 14340: schemas/util.sql: to_freq(): use util.copy() instead of util.copy_types_and_data() to avoid a dependency on util.copy_types_and_data()
Aaron Marcuse-Kubitza

07/25/2014

09:57 PM Revision 14339: fix: schemas/util.sql: copy_data(): also need to ANALYZE table after loading data into it
Aaron Marcuse-Kubitza
09:13 PM Revision 14338: schemas/public_.sql: analytical_stem_view: use viewFullOccurrence_individual_view to avoid duplicated code between the views. this moves the stem-related columns to the end of the view.
Aaron Marcuse-Kubitza
06:26 PM Revision 14337: schemas/public_.sql: added viewFullOccurrence_individual_view
Aaron Marcuse-Kubitza
06:20 PM Revision 14336: web/username_prefix.php: substitutions: also support "" because Postgres doubles " to escape them
Aaron Marcuse-Kubitza
06:17 PM Revision 14335: web/username_prefix.php: added support for substitutions ( x."_y@url -> x.x_y@url ), which can be used when a table name is repeated in a column name
Aaron Marcuse-Kubitza
06:15 PM Revision 14334: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
04:09 PM Bug #943 (New): in TNRS, the Constrain by Source option is applied incorrectly to the results download
h3. issue
from "TNRS issue 188":https://pods.iplantcollaborative.org/jira/browse/TNRS-188 (in iPlant JIRA):
> t...
Aaron Marcuse-Kubitza
02:31 PM Revision 14333: schemas/util.sql: derived_col_constraint_initially_enabled(): clarified that this is always based on whether the existing constraint is enabled
Aaron Marcuse-Kubitza
02:21 PM Revision 14332: inputs/.TNRS/schema.sql: taxon_match: COMMENT: added steps to port derived column changes to vegbiendev
Aaron Marcuse-Kubitza
02:12 PM Revision 14331: schemas/util.sql: added derived_cols_export(), which creates SQL to port the derived cols to another DB
Aaron Marcuse-Kubitza
12:41 PM Revision 14330: 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
Aaron Marcuse-Kubitza
12:14 PM Revision 14329: inputs/.TNRS/schema.sql: taxon_match: added derived column "matched~Name[_no_author]___@TNRS__@vegpath.org", which removes the "No suitable matches found." string
Aaron Marcuse-Kubitza

07/22/2014

06:50 AM Revision 14328: inputs/.TNRS/schema.sql: reordered derived columns in dependency order
Aaron Marcuse-Kubitza
06:46 AM Revision 14327: 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
Aaron Marcuse-Kubitza
06:44 AM Revision 14326: inputs/.TNRS/schema.sql: taxon_match: added derived column "[scrubbed_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org"
Aaron Marcuse-Kubitza
06:41 AM Revision 14325: bugfix: inputs/.TNRS/schema.sql: "[accepted_]genus__@DwC__@vegpath.org": need to populate this for rank = genus
Aaron Marcuse-Kubitza
05:47 AM Revision 14324: inputs/.TNRS/schema.sql: taxon_match: added derived column "[scrubbed_]taxonomicStatus__@DwC__@vegpath.org"
Aaron Marcuse-Kubitza
05:30 AM Revision 14323: 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
Aaron Marcuse-Kubitza
05:24 AM Revision 14322: bugfix: derived_col_constraints_enable(): also need to update col comments, in addition to table__fill_derived()
Aaron Marcuse-Kubitza
04:54 AM Revision 14321: schemas/util.sql: check_constraint_enabled(): made it IMMUTABLE
Aaron Marcuse-Kubitza
04:48 AM Revision 14320: bugfix: schemas/util.sql: derived_col_constraints_enable(): need to update table__fill_derived() w/ formatting changes from enabling constraints
Aaron Marcuse-Kubitza
04:40 AM Revision 14319: bugfix: schemas/util.sql: derived_col_constraints_enable(): need to update table__fill_derived() w/ formatting changes from enabling constraints
Aaron Marcuse-Kubitza
04:12 AM Revision 14318: 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
Aaron Marcuse-Kubitza
04:01 AM Revision 14317: 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
Aaron Marcuse-Kubitza
03:57 AM Revision 14316: fix: schemas/util.sql: derived_cols_populate(): documented that this function will sometimes not repopulate columns when needed, such as after changing the column order. in these cases, it is necessary to run util.derived_cols_repopulate() manually.
Aaron Marcuse-Kubitza
03:53 AM Revision 14315: schemas/util.sql: derived_cols_populate(): use new derived_cols_repopulate()
Aaron Marcuse-Kubitza
03:51 AM Revision 14314: schemas/util.sql: added derived_cols_repopulate()
Aaron Marcuse-Kubitza
03:25 AM Revision 14313: fix: inputs/.TNRS/schema.sql: taxon_match: COMMENT: to add columns in the middle: also need to run util.derived_cols_update()
Aaron Marcuse-Kubitza
03:23 AM Revision 14312: fix: inputs/.TNRS/schema.sql: taxon_match: COMMENT: updated util.derived_cols_sync() to util.derived_cols_update()
Aaron Marcuse-Kubitza
03:20 AM Revision 14311: inputs/.TNRS/schema.sql: reordered derived columns in dependency order
Aaron Marcuse-Kubitza
03:12 AM Revision 14310: inputs/.TNRS/schema.sql: reordered derived columns in dependency order
Aaron Marcuse-Kubitza
02:44 AM Revision 14309: bugfix: schemas/util.sql: derived_cols_trigger_update(): need to clear derived cols first so old values won't be used in calculations
Aaron Marcuse-Kubitza
02:36 AM Revision 14308: inputs/.TNRS/schema.sql: derived_cols_trigger_update(): put expr on same line as var, to save space
Aaron Marcuse-Kubitza
02:33 AM Revision 14307: inputs/.TNRS/schema.sql: derived_cols_trigger_update(): removed lines between statements, which add too much space
Aaron Marcuse-Kubitza
02:27 AM Revision 14306: fix: schemas/util.sql: derived_cols_trigger_update(): don't indent expr because may have multiple lines
Aaron Marcuse-Kubitza
02:25 AM Revision 14305: bugfix: schemas/util.sql: derived_col_update(): set_comment(): vars can't have same name as params, which will be substituted
Aaron Marcuse-Kubitza
01:48 AM Revision 14304: inputs/.TNRS/schema.sql: taxon_match: added derived column "[accepted_]morphospecies[_binomial]__@Brad__.TNRS@vegpath.org"
Aaron Marcuse-Kubitza
01:37 AM Revision 14303: inputs/.TNRS/schema.sql: taxon_match: added derived column "[parsed_]morphospecies[_suffix]__@Brad__.morphosp@vegpath.org"
Aaron Marcuse-Kubitza
01:27 AM Revision 14302: added web/people/Brad_Boyle/morphosp symlink to morphospecies
Aaron Marcuse-Kubitza
12:37 AM Revision 14301: added derived/TNRS/Morphospecies and scope.eml* from Brad
Aaron Marcuse-Kubitza
12:36 AM Revision 14300: added web/people/Brad_Boyle/morphospecies redirect to Morphospecies and scope.eml.txt
Aaron Marcuse-Kubitza
12:35 AM Revision 14299: added web/people/Brad_Boyle/Morphospecies and scope.eml.txt symlink
Aaron Marcuse-Kubitza
12:34 AM Revision 14298: added derived/TNRS/Morphospecies and scope.eml* from Brad
Aaron Marcuse-Kubitza
12:27 AM Revision 14297: added web/people/Brad_Boyle/TNRS redirect to Modifications to procedure to scrubbing names using TNRS.docx
Aaron Marcuse-Kubitza
12:27 AM Revision 14296: added web/people/Brad_Boyle/Modifications to procedure to scrubbing names using TNRS.docx symlink
Aaron Marcuse-Kubitza
12:18 AM Revision 14295: added derived/TNRS/Modifications to procedure to scrubbing names using TNRS.docx from Brad
Aaron Marcuse-Kubitza

07/21/2014

11:59 PM Revision 14294: schemas/public_.sql: analytical_stem: synced to analytical_stem_view
Aaron Marcuse-Kubitza
11:56 PM Revision 14293: bugfix: schemas/util.sql: view_body(): need to match view defs without trailing \n
Aaron Marcuse-Kubitza
11:53 PM Revision 14292: bugfix: schemas/util.sql: view_body(): need to support both CREATE statements and view bodies
Aaron Marcuse-Kubitza
11:23 PM Revision 14291: bugfix: schemas/util.sql: raise(): use eval_raw() so that functions called by eval() (such as view_def_to_orig()) can use raise() for debugging
Aaron Marcuse-Kubitza
09:30 PM Revision 14290: schemas/util.sql: eval(): use new eval_raw()
Aaron Marcuse-Kubitza
09:29 PM Revision 14289: schemas/util.sql: added eval_raw()
Aaron Marcuse-Kubitza
07:52 PM Revision 14288: bugfix: schemas/util.sql: view_is_automatically_updatable(), view_is_subset(): use util.view_body() so not matching COMMENT statements, etc
Aaron Marcuse-Kubitza
07:35 PM Revision 14287: schemas/util.sql: added view_body()
Aaron Marcuse-Kubitza
07:03 PM Revision 14286: bugfix: schemas/util.sql: view_is_subset(): need to support "(-x-)" in col name
Aaron Marcuse-Kubitza
06:34 PM Revision 14285: schemas/util.sql: added copy_struct(from_ regtype, to_ text) and copy_data(from_ regtype, to_ text), and use these in a general-purpose copy()
Aaron Marcuse-Kubitza
05:44 PM Revision 14284: inputs/.TNRS/schema.sql: added new derived columns to derived views
Aaron Marcuse-Kubitza
05:30 PM Revision 14283: fix: schemas/util.sql: derived_col_update(): column comment: formula: put on own line to support multiline exprs
Aaron Marcuse-Kubitza
05:26 PM Revision 14282: 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
Aaron Marcuse-Kubitza
05:13 PM Revision 14281: inputs/.TNRS/schema.sql: taxon_match: added derived columns scrubbed_*
Aaron Marcuse-Kubitza
05:03 PM Revision 14280: bugfix: schemas/util.sql: derived_col_expr_from_check_constraint(): need to handle strs with \n after IS DISTINCT FROM
Aaron Marcuse-Kubitza
04:34 PM Revision 14279: inputs/.TNRS/schema.sql: taxon_match: put matched-taxon derived columns before accepted-taxon derived columns
Aaron Marcuse-Kubitza
04:25 PM Revision 14278: inputs/.TNRS/schema.sql: taxon_match: added derived column "[matched_]species[_binomial]~(-Accepted_-)__@TNRS__@vegpath.org"
Aaron Marcuse-Kubitza
04:08 PM Revision 14277: 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
Aaron Marcuse-Kubitza
04:05 PM Revision 14276: schemas/util.sql: added derived_col_name_from_check_constraint()
Aaron Marcuse-Kubitza
03:48 PM Revision 14275: schemas/util.sql: derived_col_update(): add steps to rename column
Aaron Marcuse-Kubitza
03:42 PM Revision 14274: web/username_prefix.php: transposes: removed recommendation for vertical alignment because different quoting syntaxes, etc. make it difficult to have a consistent alignment anyway
Aaron Marcuse-Kubitza
03:34 PM Revision 14273: bugfix: schemas/util.sql: derived_col_update(): don't set_comment() until CHECK constraint exists so that we can use its canon-ed formula
Aaron Marcuse-Kubitza
03:24 PM Revision 14272: bugfix: schemas/util.sql: check_constraint_expr_enable(): don't remove suffix without also removing prefix. this is done by using extract_by_regexp() instead. also changed check_constraint_enabled() to use regexps to match this.
Aaron Marcuse-Kubitza
03:08 PM Revision 14271: bugfix: schemas/util.sql: extract_by_regexp(): needs surrounding COALESCE() in case no match
Aaron Marcuse-Kubitza
03:05 PM Revision 14270: schemas/util.sql: added extract_by_regexp()
Aaron Marcuse-Kubitza
09:02 AM Revision 14269: inputs/.TNRS/schema.sql: taxon_match: added derived column _matched_has_accepted
Aaron Marcuse-Kubitza
08:47 AM Revision 14268: inputs/.TNRS/schema.sql: added new derived columns to derived views
Aaron Marcuse-Kubitza
08:44 AM Revision 14267: inputs/.TNRS/schema.sql: taxon_match: added derived columns "[matched_]scientificName[_with_author]__@DwC__@vegpath.org", "[accepted_]scientificName[_with_author]__@DwC__@vegpath.org"
Aaron Marcuse-Kubitza
08:29 AM Revision 14266: inputs/.TNRS/schema.sql: taxon_match: added derived columns "[accepted_]Infraspecific_rank[_abbr]__@TNRS__@vegpath.org", "[accepted_]infraspecificEpithet__@DwC__@vegpath.org"
Aaron Marcuse-Kubitza
08:26 AM Revision 14265: inputs/.TNRS/schema.sql: taxon_match: added derived column "__accepted_infraspecific_{rank,epithet}"
Aaron Marcuse-Kubitza
08:19 AM Revision 14264: inputs/.TNRS/schema.sql: taxon_match: added derived column __accepted_infraspecific_label
Aaron Marcuse-Kubitza
08:12 AM Revision 14263: bugfix: schemas/util.sql: canon_sql(): need to use the right search_path
Aaron Marcuse-Kubitza
08:12 AM Revision 14262: bugfix: schemas/util.sql: check_constraint view: def: must use our wrapper so that the right search_path is used
Aaron Marcuse-Kubitza
08:08 AM Revision 14261: schemas/util.sql: added pg_get_expr() wrapper, which sets search_path to pg_temp
Aaron Marcuse-Kubitza
07:41 AM Revision 14260: bugfix: schemas/util.sql: check_constraint_expr_*(): updated strings for new Mac Postgres update, which was installed on reboot
Aaron Marcuse-Kubitza
07:40 AM Revision 14259: bugfix: schemas/util.sql: check_constraint_expr_*(): updated strings for new Mac Postgres update, which was installed on reboot
Aaron Marcuse-Kubitza
06:55 AM Revision 14258: bugfix: schemas/util.sql: derived_col_update(): steps to modify: also need to run util.derived_cols_populate()
Aaron Marcuse-Kubitza
06:54 AM Revision 14257: inputs/.TNRS/schema.sql: taxon_match: added derived columns "[accepted_]genus__@DwC__@vegpath.org", "[accepted_]specificEpithet__@DwC__@vegpath.org"
Aaron Marcuse-Kubitza
06:50 AM Revision 14256: bugfix: schemas/util.sql: check_constraint view: can't use consrc because this doesn't get auto-updated with column renames
Aaron Marcuse-Kubitza
06:37 AM Revision 14255: bugfix: schemas/util.sql: derived_col_constraints_enable(): need final `SELECT NULL::void` so don't fold away functions called in previous query
Aaron Marcuse-Kubitza
06:26 AM Revision 14254: inputs/.TNRS/schema.sql: taxon_match: ran derived_cols_update()
Aaron Marcuse-Kubitza
06:19 AM Revision 14253: bugfix: derived_col_constraint_initially_enabled(): must be both already enabled *and* unchanged to be initially enabled (r14240 was only partially correct)
Aaron Marcuse-Kubitza
06:08 AM Revision 14252: schemas/util.sql: derived_cols_trigger_update(): to regenerate instructions: use util.derived_cols_update(), which also performs other updates
Aaron Marcuse-Kubitza
06:07 AM Revision 14251: schemas/util.sql: derived_cols_sync(): renamed to derived_cols_trigger_update() for clarity
Aaron Marcuse-Kubitza
06:05 AM Revision 14250: schemas/util.sql: added derived_cols_update()
Aaron Marcuse-Kubitza
05:58 AM Revision 14249: schemas/util.sql: derived_cols_sync(): renamed to derived_cols_trigger_update() for clarity
Aaron Marcuse-Kubitza
05:54 AM Revision 14248: schemas/util.sql: derived_col_update(): add comment describing how to modify derived column
Aaron Marcuse-Kubitza
05:41 AM Revision 14247: schemas/util.sql: added quote_typed(derived_col_def)
Aaron Marcuse-Kubitza
05:37 AM Revision 14246: schemas/util.sql: added quote_typed(col)
Aaron Marcuse-Kubitza
05:14 AM Revision 14245: schemas/util.sql: derived_cols_sync(): table__fill_derived(): document in the function comment how to regenerate it
Aaron Marcuse-Kubitza
05:08 AM Revision 14244: schemas/util.sql: added mk_set_comment(regprocedure, text)
Aaron Marcuse-Kubitza
05:07 AM Revision 14243: schemas/util.sql: set_comment(): accept anything with a mk_set_comment()
Aaron Marcuse-Kubitza
03:39 AM Revision 14242: fix: schemas/util.sql: check_constraint_expr_disable(): need to use CASE instead of `true OR ` because OR always evaluates both sides, slowing down constraint evaluation
Aaron Marcuse-Kubitza
03:23 AM Revision 14241: fix: schemas/util.sql: check_constraint view: conrelid: don't cast to regclass so can use index scan
Aaron Marcuse-Kubitza
03:21 AM Revision 14240: bugfix: derived_col_constraint_initially_enabled(): use whether existing constraint is already enabled, not whether expr is unchanged (which does not affect the *enabled* status)
Aaron Marcuse-Kubitza
02:52 AM Revision 14239: schemas/util.sql: check_constraint_canon_sql(): use util.debug_print_return_value() to assist debugging
Aaron Marcuse-Kubitza
02:49 AM Revision 14238: bugfix: schemas/util.sql: check_constraint_replace(): need to use util.check_constraint_canon_sql() instead of util.canon_sql()
Aaron Marcuse-Kubitza
02:40 AM Revision 14237: schemas/util.sql: added check_constraint_canon_sql(). this must be used instead of plain util.canon_sql() because unlike queries, CHECK constraints are not simplified, just standardized.
Aaron Marcuse-Kubitza
02:06 AM Revision 14236: schemas/util.sql: check_constraint_replace(): support not canon-ing def.expr
Aaron Marcuse-Kubitza
12:23 AM Revision 14235: bugfix: schemas/util.sql: CHECK constraint exprs: need to remove the enclosing () to be consistent everywhere
Aaron Marcuse-Kubitza
 

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