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Name Size Revision Age Author Comment
  _archive 1598 over 12 years Aaron Marcuse-Kubitza Moved _archive/tapir2flatClient/trunk/client/ t...
  analysis 3076 over 12 years Aaron Marcuse-Kubitza Added top-level analysis dir for range modeling
  backups 10267 over 11 years Aaron Marcuse-Kubitza backups/Makefile: %.backup/restore: documented ...
  bin 10448 over 11 years Aaron Marcuse-Kubitza bin/my2pg: use s!...!...! when either the regex...
  config 7801 over 11 years Aaron Marcuse-Kubitza root Makefile: VegBIEN DB: mk_db: Added command...
  exports 9928 over 11 years Aaron Marcuse-Kubitza added exports/_archive/
  inputs 10494 over 11 years Aaron Marcuse-Kubitza inputs/SpeciesLink/Specimen/map.csv: conceptual...
  lib 10446 over 11 years Aaron Marcuse-Kubitza lib/sh/db.sh: mysqldump(): don't use --compatib...
  mappings 10420 over 11 years Aaron Marcuse-Kubitza mappings/VegCore.htm: regenerated from wiki. ad...
  planning 10467 over 11 years Aaron Marcuse-Kubitza planning/timeline/timeline.2013.xls: updated fo...
  schemas 10496 over 11 years Aaron Marcuse-Kubitza schemas/VegCore/VegCore.ERD.mwb: taxon_path: co...
  web 10306 over 11 years Aaron Marcuse-Kubitza web/links/index.htm: updated to Firefox bookmar...
.htaccess 326 Bytes 8771 over 11 years Aaron Marcuse-Kubitza /.htaccess: use canonical URL without symlinks
.rsync_filter.upload 33 Bytes 10042 over 11 years Aaron Marcuse-Kubitza /.rsync_ignore: temp files: hide them on upload...
.rsync_ignore 12 Bytes 10042 over 11 years Aaron Marcuse-Kubitza /.rsync_ignore: temp files: hide them on upload...
Makefile 12.6 KB 10223 over 11 years Aaron Marcuse-Kubitza /Makefile: mysql-Linux: also install mysql-work...
README.TXT 23.3 KB 10379 over 11 years Aaron Marcuse-Kubitza /README.TXT: Maintenance: added instructions fo...
fix_perms 97 Bytes 7560 almost 12 years Aaron Marcuse-Kubitza Added root fix_perms
map 1001 Bytes 6949 almost 12 years Aaron Marcuse-Kubitza vegbien_dest: Changed default $prefix to "", so...
new_terms.csv 38.1 KB 7222 almost 12 years Aaron Marcuse-Kubitza new_terms.csv: Regenerated
run 433 Bytes 9916 over 11 years Aaron Marcuse-Kubitza /run: geoscrub_input/make(): documented runtime...
unmapped_terms.csv 13.1 KB 7201 almost 12 years Aaron Marcuse-Kubitza **/new_terms.csv, **/unmapped_terms.csv: Regene...

Latest revisions

# Date Author Comment
10496 07/30/2013 06:26 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_path: converted to an auxiliary table of taxon_name instead of a subclass of it (like geopath for the place table). this causes distinct taxon_paths to be stored only once, instead of repeatedly for each taxon_name.

10495 07/30/2013 06:16 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: place hierarchy: reorganized to store scrubbed geoplaces in a containment hierarchy instead of a denormalized geopath. this allows each source-specific place to be GNRS-scrubbed to a GADM place, and then have its coordinates geovalidated to see if it is within the matched GADM place. this uses the georeferencing table to store the matched GADM place (scrubbed_geoplace) for each input place, instead of geopath_scrub to store the matched GADM geo*path* for each input geo*path*. (this avoids the need to scrub every combination of place ranks, because just the name of each place is scrubbed relative to its parent place.) geopath instead becomes an auxiliary table to store the place table's verbatim ranks, for easy access and storage.

10494 07/30/2013 04:51 PM Aaron Marcuse-Kubitza

inputs/SpeciesLink/Specimen/map.csv: conceptual_darwin_2003_1_0_BoundingBox: remapped to UNUSED

10493 07/30/2013 03:22 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: place: renamed to local_place to distinguish it from geoplace, which is not a subclass of place (it is a separate, global table, while local_place is source-specific). note that renames sometimes need to be done manually on vegbiendev, to avoid triggering a MySQL bug that blocks the new table from being created and requires the entire database to be recreated to clear the error.

10492 07/30/2013 03:02 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: stem, stem_observation: made associated individual/individual_observation optional, because some stems (e.g. in VegBank) are not grouped together into individuals. note that a stem is still considered to BE-AN individual, but it is a type of individual which may be grouped under another, plant-level individual.

10491 07/30/2013 02:47 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

10490 07/30/2013 02:45 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen_observation: added description (vegcore.vegpath.org?specimenDescription). taxon_presence: added occurrence_status (vegcore.vegpath.org?occurrenceStatus). stem_observation, aggregate_observation: made room for them to expand with additional first-class fields.

10489 07/30/2013 02:22 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_presence, taxon_absence: inherit from taxon_determination rather than taxon_observation, so that the taxon_determination's taxon can be used as the identifying taxon (i.e. the authorPlantName, VegCore.vegpath.org?authorPlantName)

10488 07/30/2013 01:41 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_determination: inherit from taxon_observation again because now that redeterminations can only occur on reobservable things, it makes sense to only allow one taxon_determination per observation event. this means that each redetermination on a specimen would get its own taxon_observation (where any additional attributes noted in the reobservation could also be included).

10487 07/30/2013 01:31 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_occurrence: renamed to reobservable to emphasize that this is only for things on which taxon redeterminations can be made, such as individuals and specimens (including voucher specimens). a redetermination on an aggregate_observation would instead be made on its voucher specimen, which is the only reobservable part of it.

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