Activity
From 06/11/2014 to 07/10/2014
07/10/2014
- 07:25 PM Revision 13974: fix: bin/import_all: updated for new metadata datasource names (see issue #940)
- 07:25 PM Revision 13973: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: updated for new metadata datasource names (see issue #940)
- 06:41 PM Task #940 (Resolved): resequence datasources in dependency order
- 04:22 PM Task #940 (Resolved): resequence datasources in dependency order
- * this enables bootstrapping the DB from a VM backup
steps
# put all [[VegBIEN_contents#datasources|metadata da... - 06:32 PM Revision 13972: fix: inputs/IUCN/: renamed to inputs/.IUCN/ (see issue #940)
- 06:04 PM Revision 13971: fix: inputs/newWorld/: renamed to inputs/.newWorld/ (see issue #940)
- 04:59 PM Revision 13970: 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.
- 03:52 PM Revision 13969: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: set up the VM: added steps to create a VM snapshot when done
- 03:37 PM Revision 13968: config/VirtualBox_VMs/vegbiendev/README.TXT: `make`: documented runtime (15 min)
- 03:33 PM Revision 13967: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: removed non-applicable step about the MySQL root password, which is not used for this procedure
- 03:32 PM Revision 13966: added config/VirtualBox_VMs/vegbiendev/README.TXT with instructions to test the import
- 12:17 PM Revision 13965: 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.
- 10:57 AM Revision 13964: fix: inputs/Madidi/LocationObservation/postprocess.sql: parse Spanish dates
- 09:45 AM Revision 13963: validation/completeness/BIENDatesPopulated.xlsx: updated: Martha added Priority column
- 08:41 AM Revision 13962: schemas/util.sql: replace_words(): use map_words() to enable inlining the concatenated hstore, so that it doesn't need to be concatenated on *each* function call
- 08:39 AM Revision 13961: schemas/util.sql: added map_words()
- 08:16 AM Revision 13960: schemas/util.sql: added date_from_spanish()
- 08:13 AM Revision 13959: schemas/util.sql: added replace_words()
- 08:09 AM Revision 13958: schemas/util.sql: added words(text)
- 08:02 AM Revision 13957: schemas/util.sql: spanish_date_words(): switched to using hstore because this is better for the algorithm that will translate these
- 07:20 AM Revision 13956: schemas/util.sql: added spanish_date_words()
- 07:19 AM Revision 13955: schemas/util.sql: added `replacement` type
- 04:09 AM Revision 13954: bugfix: mk_set_relation_metadata(): need to include col comments as well so that these are re-created properly by recreate()
- 04:07 AM Revision 13953: schemas/util.sql: added mk_set_comments(regclass)
- 04:06 AM Revision 13952: schemas/util.sql: show_set_comment(regclass): renamed to mk_set_comment() to match other mk_set_comment() functions
- 04:01 AM Revision 13951: schemas/util.sql: added mk_set_col_comments(regclass)
- 03:58 AM Revision 13950: schemas/util.sql: added cols(regclass)
- 03:56 AM Revision 13949: schemas/util.sql: added mk_set_comment(col_ref)
- 03:18 AM Revision 13948: added validation/completeness/BIENDatesPopulated.xlsx from Google spreadsheets
07/09/2014
- 02:50 PM Revision 13947: fix: mappings/VegCore-VegBIEN.csv: mapped DwC year/month/day, which are split-date alternatives to eventDate. this fixes the missing eventDate in FIA.
- 02:45 PM Revision 13946: bugfix: inputs/FIA/*/VegBIEN.csv: regenerated, replacing these with symlinks to the file used by new-style import
- 02:34 PM Revision 13945: inputs/FIA/taxon_observation.**/test.xml.ref: updated
- 02:34 PM Revision 13944: inputs/FIA/TREE/test.xml.ref: updated
- 02:29 PM Revision 13943: inputs/FIA/REF_RESEARCH_STATION/test.xml.ref: updated
- 02:13 PM Revision 13942: bugfix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: updated to new TWiki/ location
- 02:12 PM Revision 13941: bugfix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: updated to new VegBIEN/ location
- 12:14 PM Revision 13940: fix: inputs/bien2_traits/TraitObservation/map.csv: mapped VisitingDate to eventDate
- 12:05 PM Revision 13939: fix: inputs/Madidi/LocationObservation/postprocess.sql: populated missing eventDate from PlotInventoryName (authorEventCode)
- 09:40 AM Revision 13938: schemas/util.sql: mk_set_comment(table_ regclass, comment text): use new util.mk_set_comment(text, text)
- 09:38 AM Revision 13937: schemas/util.sql: added mk_set_comment(col col_ref, comment text)
- 09:37 AM Revision 13936: schemas/util.sql: added sql(col_ref)
- 09:35 AM Revision 13935: schemas/util.sql: added mk_set_comment(on_ text, comment text)
- 07:53 AM Revision 13934: schemas/util.sql: added comment(col_ref)
- 07:50 AM Revision 13933: schemas/util.sql: added col_num(col_ref)
- 07:03 AM Revision 13932: removed no longer needed inputs/.TNRS/grants.sql, since the grants in schema.sql are now being run
- 07:03 AM Revision 13931: 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
- 06:22 AM Revision 13930: schemas/public_.sql: iucn_red_list_view: documented how to regenerate iucn_red_list from this
07/08/2014
- 04:17 PM Revision 13929: exports/2014-6-4.Iara_Lacher.reserve_prioritization.csv.run: documented runtime (7.5 min) and rowcount (3.5 million)
- 03:23 PM Revision 13928: bugfix: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: fixed slowdown in materializing the view, which was caused by source__observation_type(), by replacing this with a LEFT JOIN as was done for is_threatened_iucn
07/07/2014
- 07:33 AM Revision 13927: schemas/util.sql: in_south_america(): optimized by using BETWEEN instead of util.contained_within__no_dateline(). this reduces the filter time for 2014-6-4.Iara_Lacher.reserve_prioritization by about 10%.
- 07:26 AM Revision 13926: fix: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: is_threatened_iucn: generate this much faster by doing a LEFT JOIN, which can reuse the same in-memory hash index for every row
- 07:04 AM Revision 13925: bugfix: schemas/public_.sql: wrapper functions can't use util-schema types because these will cause the wrapper function to be cascadingly dropped when the util schema is reinstalled
- 06:55 AM Revision 13924: bugfix: in_south_america(): must use util.contained_within__no_dateline() instead of util.contained_within_approx() to ensure that the more accurate geometry logic is used
- 06:51 AM Revision 13923: bugfix: schemas/public_.sql: source__observation_type(): don't display NOTICEs about the search_path, because this function will be called millions of times
- 06:48 AM Revision 13922: bugfix: schemas/public_.sql: in_iucn_red_list(): don't display NOTICEs about the search_path, because this function will be called millions of times
- 06:43 AM Revision 13921: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added is_threatened_iucn
- 06:37 AM Revision 13920: schemas/public_.sql: added in_iucn_red_list()
- 06:36 AM Revision 13919: schemas/public_.sql: added iucn_red_list, materialized from iucn_red_list_view
- 06:22 AM Revision 13918: bugfix: schemas/vegbien.sql: iucn_red_list_view: need to include only names with an accepted name, and distinctify on the accepted names
- 06:17 AM Revision 13917: schemas/public_.sql: added iucn_red_list
- 06:14 AM Revision 13916: schemas/util.sql: materialize_view(): use util.copy() instead of util.materialize_query() so that all view metadata is transferred
- 06:02 AM Revision 13915: schemas/public_.sql: iucn_red_list: renamed to iucn_red_list_view since this will be materialized
- 06:01 AM Revision 13914: schemas/public_.sql: added iucn_red_list
- 05:44 AM Revision 13913: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added collection_type (using source__observation_type())
- 05:36 AM Revision 13912: schemas/public_.sql: added source__observation_type()
- 05:04 AM Revision 13911: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added accepted_subspecies, and removed accepted_taxon_name_with_author which had been substituting for it
- 04:50 AM Revision 13910: schemas/public_.sql: added subspecies() wrapper
- 04:38 AM Revision 13909: schemas/util.sql: added subspecies()
- 04:10 AM Revision 13908: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: include only coordinates in South America
- 03:55 AM Revision 13907: schemas/util.sql: added south_america(), in_south_america()
- 03:37 AM Revision 13906: fix: schemas/util.sql: OPERATOR ~@(geocoord, postgis.geometry): renamed to @ because this is not an approximate comparison for geometry
- 03:35 AM Revision 13905: fix: schemas/util.sql: contained_within_approx(geocoord, postgis.geometry): renamed to contained_within__no_dateline(__) because this is not an approximate comparison for geometry
- 03:30 AM Revision 13904: schemas/util.sql: lat_long_in_new_world(): renamed to just in_new_world() because the lat/long is implied by the param type
- 03:08 AM Revision 13903: schemas/util.sql: lat_long_in_new_world(): take a geocoord param instead of separate lat/long params
- 03:00 AM Revision 13902: backups/TNRS.backup.md5: updated
07/06/2014
- 11:08 PM Revision 13901: schemas/util.sql: added contained_within_approx(geocoord, geometry) and corresponding OPERATOR ~@(geocoord, geometry)
- 10:39 PM Revision 13900: schemas/util.sql: added OPERATOR ~@(geocoord, geography)
- 10:23 PM Revision 13899: schemas/util.sql: lat_long_in_new_world(): use new contained_within_approx(geocoord, geography)
- 10:17 PM Revision 13898: schemas/util.sql: added contained_within_approx(geocoord, postgis.geography), which enables specifying just `(lat, long)` without the ::util.geocoord type specifier
- 04:04 PM Revision 13897: schemas/util.sql: OPERATOR @(postgis.geography, postgis.geography): renamed to ~@ because it's approximate
- 03:52 PM Revision 13896: schemas/util.sql: contained_within(): renamed to contained_within_approx() because the latitude lines of geography type bounding boxes bulge outward, creating false positives above and below the bounding box
- 03:50 PM Revision 13895: schemas/util.sql: added contained_within__no_dateline(geometry, geometry) and corresponding operator @
- 02:51 PM Revision 13894: schemas/util.sql: contained_within(): renamed to contained_within_approx() because the latitude lines of geography type bounding boxes bulge outward, creating false positives above and below the bounding box
- 05:49 AM Revision 13893: schemas/util.sql: geometry(geocoord): documented that it is not possible to create a cast for this, as a bug in pg_dump prevents the cast from being exported, even when no export filters are applied
07/05/2014
- 12:40 PM Revision 13892: schemas/util.sql: point(geocoord): renamed to geometry(geocoord) since this is now a cast
- 12:03 PM Revision 13891: schemas/util.sql: point(): return geometry instead of geography to support using points with geometry arithmetic
- 11:24 AM Revision 13890: schemas/util.sql: point(): take a single util.geocoord param instead of separate lat/long
- 10:45 AM Revision 13889: schemas/util.sql: added geocoord type
07/04/2014
- 08:29 PM Revision 13888: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: include only *georeferenced* occurrences (lat/long NOT NULL)
- 08:25 PM Revision 13887: schemas/util.sql: bounding_box(): use bounding_box__no_dateline() to construct the postgis.geometry object
- 08:23 PM Revision 13886: schemas/util.sql: added bounding_box__no_dateline(), which is more accurate than util.bounding_box() (latitude lines will be straight), but geocoordinate wraparound is not supported
- 08:14 PM Revision 13885: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added functional traits that we have 1st-class columns for (dbh_cm, height_m)
- 12:29 PM Revision 13884: added exports/2014-6-4.Iara_Lacher.reserve_prioritization.csv.run
- 11:12 AM Revision 13883: inputs/publishable datasources.xlsx: updated
- 08:45 AM Revision 13882: inputs/publishable datasources.xlsx: updated
07/03/2014
- 08:13 PM Revision 13881: 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
- 09:59 AM Revision 13880: planning/meetings/BIEN conference call availability.xlsx: updated
- 03:47 AM Task #917: TNRS: Instructions for new version with TPL
- a single "-" creates strikethrough formatting, so you have to use "--" instead
- 12:34 AM Revision 13879: 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
- 12:17 AM Revision 13878: fix: inputs/.TNRS/schema.sql: MatchedTaxon: use taxon_best_match instead of taxon_match because this should provide only one match per taxon
07/02/2014
- 02:17 AM Revision 13877: bugfix: /README.TXT: Mac settings backup: backup to jupiter: need to exclude ~/software/**/.svn/ because these are different on jupiter
- 02:00 AM Revision 13876: /README.TXT: Mac settings backup: backup to jupiter: removed no longer applicable exclude of /VirtualBox VMs/Ubuntu/Ubuntu.vdi
06/27/2014
- 03:15 PM Task #917: TNRS: Instructions for new version with TPL
- test update now that watcher notifications have been fixed
06/26/2014
- 06:30 PM Revision 13875: inputs/.TNRS/schema.sql: added taxon_best_match view
- 06:12 PM Revision 13874: inputs/.TNRS/schema.sql: taxon_match: added taxon_match__one_selected_match unique index
- 05:06 PM Revision 13873: backups/TNRS.backup.md5: updated
- 09:49 AM Revision 13872: planning/meetings/BIEN conference call availability.xlsx: updated
- 09:25 AM Task #917: TNRS: Instructions for new version with TPL
- testing Martha's watcher notifications again after e-mail address fix...
- 09:23 AM Task #917: TNRS: Instructions for new version with TPL
- testing Martha's watcher notifications...
- 05:41 AM Revision 13871: inputs/.TNRS/schema.sql: taxon_match__fill(): split into separate DECLARE blocks for each field for clarity
- 04:58 AM Revision 13870: inputs/.TNRS/data.sql: refreshed
- 04:57 AM Revision 13869: fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*
- 04:33 AM Revision 13868: fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*
- 04:28 AM Revision 13867: inputs/.TNRS/data.sql: refreshed
- 04:11 AM Revision 13866: 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
- 02:43 AM Revision 13865: fix: schemas/Makefile: vegbien.sql: also need to update inputs/.TNRS/data.sql, since its contents change along with this
- 02:41 AM Revision 13864: 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
- 02:39 AM Revision 13863: 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
- 02:38 AM Revision 13862: 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
- 02:14 AM Revision 13861: 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
06/25/2014
- 07:54 PM Revision 13860: lib/tnrs.py: dirty: documented that this actually used to be on in the web app (see r9910, 2013-6-18), but does not appear to be needed (the source_sorting bug alluded to in r9910 is not fixed by enabling the dirty setting)
- 07:48 PM Task #917: TNRS: Instructions for new version with TPL
- multiple @Selected@ names bug fixed in r13855
- 07:46 PM Revision 13859: lib/tnrs.py: requests: also debug-print request URL
- 07:44 PM Revision 13858: lib/tnrs.py: Download: include the same debug info as do_request()
- 07:41 PM Revision 13857: lib/tnrs.py: do_request(): also debug-print request headers
- 07:39 PM Revision 13856: lib/tnrs.py: download_request_template: dirty: documented why this must be off
- 07:36 PM Revision 13855: bugfix: lib/tnrs.py: download_request_template: fixed bug where multiple names were being marked as Selected, because dirty was incorrectly set to true unlike in the web app
- 07:30 PM Revision 13854: added derived/TNRS/web_app/protocol/
- 04:28 PM Revision 13853: inputs/.TNRS/data.sql: refreshed
- 04:25 PM Revision 13852: 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
- 03:47 PM Revision 13851: inputs/.TNRS/schema.sql: tnrs: renamed to tnrs_match to distinguish it from other TNRS-related tables
- 03:33 PM Revision 13850: inputs/.TNRS/schema.sql: tnrs: renamed to tnrs_match to distinguish it from other TNRS-related tables
- 02:38 PM Revision 13849: fix: lib/phpPgAdmin.login.php.diff: use relative file path rather than the path the file was at when the patch was created
- 02:34 PM Revision 13848: /Makefile, lib/phpPgAdmin.login.php.diff: public_ user: added auto-filled password so that users would not be confused as to what to type in the password field
- 02:15 PM Revision 13847: added schemas/VegCore/phpMyAdmin/libraries/plugins/auth/AuthenticationCookie.class.php.diff
- 01:19 PM Task #938 (New): Enquist's taxon validation
- From Brian Enquist:
I can start by checking the accuracy of the fields, and data for a random subset of plots. To ... - 10:39 AM Revision 13846: inputs/.TNRS/schema.sql: `taxon_scrub.scrubbed_unique_taxon_name.*`: added to-modify instructions
- 10:36 AM Revision 13845: 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
- 10:21 AM Revision 13844: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB
- 05:15 AM Revision 13843: schemas/public_.sql: analytical_stem_view and related views: updated COMMENTs from data dictionary spreadsheet, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#copy-data-dictionary-definitions-to-database
- 04:11 AM Revision 13842: schemas/public_.sql: ran analytical_stem_view_modify(), which transfers the column COMMENTs from analytical_stem_view to analytical_stem
- 04:04 AM Revision 13841: bugfix: schemas/util.sql: view_def_to_orig(): need to handle cases when list of cols from the same table is not an expanded * expression
- 03:59 AM Revision 13840: schemas/util.sql: added view_is_subset(view_def text)
- 03:58 AM Revision 13839: schemas/util.sql: added view_is_automatically_updatable(view_def text)
- 03:23 AM Revision 13838: bugfix: schemas/util.sql: show_create_view(): use the overridden version of pg_get_viewdef(), which supports expanded * expressions. this was possibly being used already whenever util happened to be in the search_path.
06/24/2014
- 05:03 PM Revision 13837: bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to new analytical_stem_view column names
- 05:01 PM Revision 13836: fix: schemas/public_.sql: analytical_stem_view derived and related views: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database but with the current columns of analytical_stem as the left-hand column
- 04:36 PM Revision 13835: bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to new analytical_stem_view column names
- 04:34 PM Revision 13834: schemas/public_.sql: analytical_stem_view: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database
- 03:27 PM Revision 13833: lib/tnrs.py: source_sorting (Constrain by Source): documented the different behavior for this in each match mode (all-matches and best-match)
06/20/2014
06/19/2014
- 04:13 PM Revision 13831: bugfix: web/.phpPgAdmin/.htaccess: : handlers: use `chain` to only run them when the RewriteRule they apply to is run
- 04:11 PM Revision 13830: web/.phpPgAdmin/.htaccess: schema : handler: removed `env=subject:schema` because that has already been set
- 04:08 PM Revision 13829: web/.phpPgAdmin/.htaccess: tables: added : suffix handler
- 04:06 PM Revision 13828: bugfix: web/.phpPgAdmin/.htaccess: view : match: moved to right after `view=` because it only applies to views, not functions
- 03:58 PM Revision 13827: web/.phpPgAdmin/.htaccess: schema: page: indicate by prefixing with : to avoid needing to explicitly list all possible pages
- 03:54 PM Revision 13826: web/.phpPgAdmin/.htaccess: table: action: indicate by prefixing with : to avoid needing to explicitly list all possible actions
- 11:13 AM Revision 13825: exports/2014-6-12.Jeff_Ott.climatic_range_determinants.csv.run: updated export_() runtime (35 min) and rowcount (23 million)
- 11:00 AM Task #916: Taxon name validation: VegBank
- most bugs fixed, just needs TNRS bug workaround
- 02:33 AM Revision 13824: fix: /README.TXT: Full database import: disk space: removed instructions to rerun the import if the disk space gets used up, because this is actually a bug and is *not* generally "fixed just by rerunning the import"
- 02:27 AM Revision 13823: schemas/util.sql: lat_long_in_new_world(): use function rather than operator+search_path to allow inlining, which enables util.new_world() to only be evaluated once
- 02:24 AM Revision 13822: bugfix: schemas/util.sql: operator @(postgis.geography, postgis.geography): must use wrapper function because st_coveredby() needs postgis to be in the search_path
- 01:57 AM Revision 13821: fix: lib/runscripts/extract.run: export_(): explicitly prevent files from becoming web-accessible, to protect against an incorrect umask in the calling process
- 01:45 AM Revision 13820: fix: schemas/util.sql: point(): hide benign "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" notices
06/18/2014
- 08:56 PM Revision 13819: schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: also include New World occurrences by coordinates, using new lat_long_in_new_world(). this modification (as requested by Jeff) will help reduce the false negatives filtered out by including only data with placenames.
- 08:52 PM Revision 13818: schemas/public_.sql: added lat_long_in_new_world() wrapper around util.lat_long_in_new_world()
- 08:49 PM Revision 13817: schemas/util.sql: lat_long_in_new_world(): documented that this includes false positives above and below the New World bounding box, as described in util.bounding_box()
- 08:44 PM Revision 13816: schemas/util.sql: bounding_box(): documented that the geography type stores all edges as arcs of great circles, resulting in the latitude lines bulging outward from the true bounding box. this will create false positives above and below the bounding box.
- 08:38 PM Revision 13815: schemas/util.sql: added lat_long_in_new_world()
- 08:35 PM Revision 13814: schemas/util.sql: added operator @(postgis.geography, postgis.geography). can't use && for this because it only compares 2D bounding boxes (which are geometry objects that do not support geocoordinate wraparound).
- 08:06 PM Revision 13813: schemas/util.sql: added point()
- 08:00 PM Revision 13812: schemas/util.sql: new_world(): removed no longer needed cast to postgis.geography
- 07:59 PM Revision 13811: bugfix: schemas/util.sql: bounding_box(): must use postgis.geography (instead of postgis.geometry) because that handles geocoordinate wraparound correctly
- 07:52 PM Revision 13810: bugfix: schemas/util.sql: bounding_box(): need to explicitly set SRID to make sure the correct value is used
- 07:39 PM Revision 13809: bugfix: schemas/util.sql: bounding_box(): use st_makeenvelope() instead of st_makebox2d() because st_makebox2d() doesn't support geocoordinate wraparound (it is not SRID-aware)
- 07:32 PM Revision 13808: schemas/util.sql: new_world(): removed no longer needed cast to postgis.geometry
- 07:31 PM Revision 13807: schemas/util.sql: bounding_box(): return postgis.geometry instead of postgis.box2d because box2d is not directly used in postgis functions
- 07:12 PM Revision 13806: bugfix: /Makefile: mk_db: plpython3u: use CREATE EXTENSION instead of createlang so that the plpython3u extension is created in addition to the plpython3u language (as it is on Linux)
- 04:43 PM Revision 13805: schemas/util.sql: added new_world()
- 04:30 PM Revision 13804: bugfix: schemas/util.sql: bounding_box(): use util.range instead of numrange to support wraparound ranges for geocoordinates
- 04:26 PM Revision 13803: schemas/util.sql: range(numeric, numeric): use util.range instead of numrange to support wraparound ranges (which use a modulus system such as geocoordinates)
- 04:20 PM Revision 13802: schemas/util.sql: added `range` type (and cast to numrange), which allows wraparound ranges such as for geocoordinates
- 03:56 PM Revision 13801: schemas/util.sql: bounding_box(): documented usage
- 03:53 PM Revision 13800: schemas/public_.sql, inputs/.TNRS/schema.sql: upgraded to Postgres 9.3.4 format, which removes trailing " "
- 03:52 PM Revision 13799: schemas/util.sql: added bounding_box()
- 03:41 PM Revision 13798: bugfix: /Makefile: postgis schema: also need to make it accessible to non-superusers
- 03:12 PM Revision 13797: /Makefile, /README.TXT: PostgreSQL: Mac OS X: switched to using homebrew, which supports PostGIS
- 01:53 PM Task #917: TNRS: Instructions for new version with TPL
- all the taxon names have now been rescrubbed
- 01:40 PM Revision 13796: backups/TNRS.backup.md5: updated
06/17/2014
- 05:25 PM Task #935 (Resolved): TNRS crashes when scrubbing names with two infraspecific epithets
- iPlant fixed this
- 04:48 PM Revision 13795: schemas/util.sql: range(numeric, numeric): use simpler numrange() constructor instead of text input syntax
- 04:39 PM Revision 13794: schemas/util.sql: operator functions: renamed to plain-text names to follow the Postgres convention of making the function name be the human-readable name of the operator
- 04:26 PM Revision 13793: fix: bin/in_place: usage: removed duplicate copy of [preserve_mtime=1]
- 04:22 PM Revision 13792: /Makefile: removed no longer used nonApacheOnPort80 code
- 04:13 PM Revision 13791: bugfix: /Makefile: phppgadmin-Linux: don't change the Apache port if something "else" is running on port 80, because this feature was only needed when tomcat was running on that port, but is now buggy
06/16/2014
- 06:50 PM Revision 13790: schemas/util.sql: added ~ operator for ranges
- 04:35 PM Revision 13789: /Makefile: mk_db: added PostGIS so it can be used by our functions
- 04:34 PM Revision 13788: bugfix: /Makefile: postgres-Linux: postgis: updated apt-get target names for Ubuntu 14.04
- 03:52 PM Revision 13787: **/LICENSE.TXT: use lowercase when there is a single set of *__*
- 03:50 PM Revision 13786: /LICENSE.TXT: refers to: removed trunk/ because of course it also applies to the branches/ and tags/ subdirs
- 02:13 PM Revision 13785: schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: allow geovalid_bien = NULL to enable filtering New World status by coordinates rather than country
- 02:03 PM Revision 13784: schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: added geovalid_bien
06/13/2014
- 08:34 PM Revision 13783: web/util.js: removed no longer used parse_dot_path(), etc. this is handled by web/.htaccess instead.
- 08:24 PM Revision 13782: web/index.php: Brad: added attribution/
- 08:22 PM Revision 13781: web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.
- 08:21 PM Revision 13780: web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.
- 08:11 PM Revision 13779: web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs
- 08:11 PM Revision 13778: web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs
- 08:08 PM Revision 13777: added web/people/Brad_Boyle/identifiers
- 08:07 PM Revision 13776: bugfix: web/index.php: Brad: updated resource names to match filesystem
- 07:58 PM Revision 13775: bugfix: web/index.php: Brad: fixed URL base
- 07:57 PM Revision 13774: web/index.php: sources: reordered/recategorized to match the subdirs and wiki.vegpath.org/VegCore
- 07:56 PM Revision 13773: schemas/VegCore/.htaccess: RewriteBase: use full path
- 07:43 PM Revision 13772: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 07:08 PM Revision 13771: schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/
- 07:06 PM Revision 13770: added web/people/Brad_Boyle/identifier_examples, which is used by the VegBIEN data dictionary
- 07:02 PM Revision 13769: placed web/BIEN3/TWiki/lib/LocalSite.cfg under version control because it contains absolute paths that need to be maintained
- 07:01 PM Revision 13768: web/main.conf: updated paths
- 06:34 PM Revision 13767: web/people/Brad_Boyle/*/.htaccess: set the destination filename using RewriteRule env, to allow escaping " " with "\ " instead of the difficult-to-read "\%20"
- 06:20 PM Revision 13766: web/people/Brad_Boyle/*/.htaccess: use relative paths to new symlinks to avoid hardcoding paths
- 06:07 PM Revision 13765: web/BIEN3/TWiki/twiki.conf: updated paths
- 05:51 PM Revision 13764: bugfix: /README.TXT: Installation: Check out svn: need to use trunk instead of root
- 05:49 PM Revision 13763: *: use vegbiendev:/home/bien instead of /home/bien/svn
- 05:15 PM Revision 13762: web/people/Brad_Boyle/: added symlinks to Brad's files that are used in the data dictionaries
- 04:29 PM Revision 13761: schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/
- 04:11 PM Revision 13760: schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
- 04:09 PM Revision 13759: web/BIEN3/Redmine/svn/.htaccess: removed unneeded RewriteBase because this does not use a relative redirect with ../
- 04:07 PM Revision 13758: schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
- 04:02 PM Revision 13757: schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
- 04:01 PM Revision 13756: schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
- 03:58 PM Revision 13755: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 03:40 PM Revision 13754: web/BIEN3: link to Redmine instead of directly to the wiki, since the Redmine/ dir should manage where BIEN3 default-redirects to
- 03:26 PM Revision 13753: schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/
- 02:20 PM Revision 13752: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 02:20 PM Revision 13751: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 02:18 PM Revision 13750: schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/
- 02:10 PM Revision 13749: schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/
- 02:01 PM Revision 13748: added schemas/VegBIEN/data_dictionary/create_bien3_viewFullOccurrence.txt from Brad
- 01:58 PM Revision 13747: schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/
- 01:26 PM Revision 13746: added schemas/VegBIEN/data_dictionary/schema_docum.pptx from Brian McGill
- 01:16 PM Revision 13745: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 01:03 PM Revision 13744: removed no longer needed inputs/VegBIEN/fs symlink. use web/.fs instead.
- 12:56 PM Revision 13743: web/.fs: changed to point directly to the svn root, so that the VegBIEN dir does not contain any recursive symlinks
- 10:51 AM Revision 13742: /README.TXT: Mac settings backup: to Dropbox: stop Dropbox beforehand to prevent Dropbox from trying to capture filesystem events while syncing
- 10:18 AM Revision 13741: /README.TXT: Mac settings backup: exclude ~/Library/Thunderbird/Profiles/9oo8rcyn.default/global-messages-db.sqlite because this file does not sync (issue #907)
- 08:45 AM Revision 13740: web/links/index.htm: updated to Firefox bookmarks: oXygen XML editor: added download link for the version (13.2) that works with NCEAS's license. bash: added fix to enable Ctrl+Arrow to work. GVFS: added links for file permissions bug. iPlant: added Atmosphere/Data Store links. Quick links: updated vegpath.org link to `vegpath.org.`.
06/12/2014
- 08:03 PM Revision 13739: web/username_prefix.php: username/password prompt message: added instructions to always append "." when visiting the homepage of the site ("vegpath.org.")
- 07:10 PM Revision 13738: schemas/VegBIEN/VegBIEN data dictionary.xlsx: moved to schemas/VegBIEN/data_dictionary/
- 05:42 PM Revision 13737: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: analytical_stem_view: approved by/to discuss: renamed to * (removing "approved by") because the participants in today's conference call indicated that they were happy with the definitions, and the issues raised before the call had been addressed
- 05:32 PM Revision 13736: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added all tables used to create analytical_stem_view, not just those that Brian M listed. (Brian M generated his tables list from the analytical_stem_view columns rather than the joins, and renamed plot.** to plot, which is why his list ended up missing tables and in the wrong order.)
- 03:56 PM Revision 13735: added exports/2014-6-12.Jeff_Ott.climatic_range_determinants.csv.run
- 03:53 PM Revision 13734: schemas/vegbien.sql: added 2014-6-12.Jeff_Ott.climatic_range_determinants (wiki.vegpath.org/Data_requests)
- 03:38 PM Revision 13733: web/username_prefix.php: deletion comments: require -...- strikethrough on both () to avoid ambiguity when the deleted part starts or ends with -
- 11:51 AM Revision 13732: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: resized columns to fit laptop screen
- 10:43 AM Revision 13731: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added my and Brian McGill's notes from the data dictionary conference call
- 10:11 AM Task #937 (New): fix missing date fields
- * -do a search for null date fields to figure out which datasources this applies to- _see "missing dates spreadsheet"...
- 08:00 AM Revision 13730: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added analytical_stem_view table definitions
- 07:38 AM Revision 13729: removed schemas/vegbien.ERD.MySQL_Workbench_6.1.6.mwb, because vegbien.ERD.mwb is now targeted to the correct version of MySQL Workbench (and is more up-to-date)
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