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Name Size Revision Age Author Comment
  _archive 1598 almost 13 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 10442 over 11 years Aaron Marcuse-Kubitza bin/my2pg: added instructions for regenerating ...
  config 7801 almost 12 years Aaron Marcuse-Kubitza root Makefile: VegBIEN DB: mk_db: Added command...
  exports 9928 over 11 years Aaron Marcuse-Kubitza added exports/_archive/
  inputs 10436 over 11 years Aaron Marcuse-Kubitza inputs/SpeciesLink/Specimen/map.csv: remapped D...
  lib 10440 over 11 years Aaron Marcuse-Kubitza bugfix: lib/sh/util.sh: $sed_cmd: make output u...
  mappings 10420 over 11 years Aaron Marcuse-Kubitza mappings/VegCore.htm: regenerated from wiki. ad...
  planning 10429 over 11 years Aaron Marcuse-Kubitza planning/timeline/timeline.2013.xls: Adding der...
  schemas 10438 over 11 years Aaron Marcuse-Kubitza schemas/VegCore/VegCore.ERD.mwb: taxon_string: ...
  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 about 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
10442 07/26/2013 05:56 PM Aaron Marcuse-Kubitza

bin/my2pg: added instructions for regenerating *.schema.sql whenever this script is changed

10441 07/26/2013 05:22 PM Aaron Marcuse-Kubitza

bin/my2pg: COMMENT: also match COMMENTs with embedded ', because there will only be one COMMENT per line, so the contents of the COMMENT can just extend to the last ' on the line

10440 07/26/2013 05:16 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/util.sh: $sed_cmd: make output unbuffered, so that running e.g. bin/my2pg at the command line produces output as each line is read

10439 07/26/2013 04:29 PM Aaron Marcuse-Kubitza

bin/my2pg: replace MySQL ` quotes with " quotes to support exports that were generated without ANSI_QUOTES mode. (this replacement only applies to schema exports, not data.) ANSI_QUOTES is only available with mysqldump --compatible modes that also include NO_TABLE_OPTIONS, which omits important table options such as comments. in particular, these comments are part of schemas/VegCore/VegCore.ERD.mwb but were not being included in VegCore.my.sql.

10438 07/26/2013 01:41 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_string: removed parsed_taxon_assertion field, since there may be more than one parsing (TNRS result) for a given taxon_string. the parsing relationship can better be represented by adding a parsed_taxon_assertion whose taxon_assertion.string points to the parsed taxon_string. getting the parsed_taxon_assertion for a taxon_string now requires joining on parsed_taxon_assertion using a backwards instead of forwards fkey, and filtering the corresponding assertions to include only the ones for TNRS (of the desired TNRS version). documented that taxon_assertion.string was previously the concatenated matched name, but is now the TNRS input name. the concatenated matched name is still in parsed_taxon_assertion.matched_taxon_concept->:taxon_name.unique_name.

10437 07/26/2013 01:22 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.my.sql: regenerated from .mwb schema, which apparently reverses the order of the fkeys (possibly a Linux MySQL bug?)

10436 07/26/2013 12:26 PM Aaron Marcuse-Kubitza

inputs/SpeciesLink/Specimen/map.csv: remapped Darwin Core synonyms to DUPLICATE. this avoids the need to translate these to postprocessing derived columns for new-style import, and also speeds up column-based import because there are less automatic alts to perform to resolve filter-less collisions. the svn diff was verified by replacing DUPLICATE#of:dwc_terms<term>#... with <term>, removing the comment, and checking that this removes the diff (except where VegCore has renamed a DwC term).

10435 07/26/2013 12:17 PM Aaron Marcuse-Kubitza

bugfix: inputs/SpeciesLink/Specimen/map.csv: *scientificName: remapped to scientificName instead of taxonName to match the DwC term's name (this is the same dwc_terms_scientificName mismapping that was fixed in r10434)

10434 07/26/2013 11:56 AM Aaron Marcuse-Kubitza

bugfix: inputs/SpeciesLink/Specimen/map.csv: dwc_terms_scientificName: remapped to scientificName instead of taxonName to match that DwC term name, as well as the mappings of other *scientificName terms

10433 07/26/2013 11:06 AM Aaron Marcuse-Kubitza

inputs/SpeciesLink/Specimen/map.csv: marked dwc_geospatial_VerbatimLatitude,Longitude as exact duplicates of dwc_terms_*

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