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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 4751 over 12 years Aaron Marcuse-Kubitza backups/Makefile: Backups: Full DB: Specify the...
  bin 5126 over 12 years Aaron Marcuse-Kubitza tnrs_db: Exclude taxonomic names which have alr...
  config 272 about 13 years Aaron Marcuse-Kubitza Moved bien_password to new config dir
  inputs 5133 over 12 years Aaron Marcuse-Kubitza inputs/.TNRS/tnrs/map.csv: Mapped columns for c...
  lib 5129 over 12 years Aaron Marcuse-Kubitza sql_io.py: cleanup_table(): Don't clean up the ...
  mappings 5132 over 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv, VegCore.csv: Remo...
  schemas 5134 over 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: taxonpath: Added back data...
  to_do 4524 over 12 years Aaron Marcuse-Kubitza to_do/timeline.doc: Updated to reflect addition...
  validation 4523 over 12 years Aaron Marcuse-Kubitza Added validation/
Makefile 9.99 KB 4752 over 12 years Aaron Marcuse-Kubitza root Makefile: PostgreSQL: postgres-Linux: Adde...
README.TXT 11.3 KB 5040 over 12 years Aaron Marcuse-Kubitza README.TXT: Data import: Starting column-based ...
map 1.28 KB 4981 over 12 years Aaron Marcuse-Kubitza root map: Fixed custom public schema override t...
new_terms.csv 30.4 KB 4887 over 12 years Aaron Marcuse-Kubitza Regenerated root unmapped_terms.csv, new_terms.csv
unmapped_terms.csv 5.8 KB 4887 over 12 years Aaron Marcuse-Kubitza Regenerated root unmapped_terms.csv, new_terms.csv

Latest revisions

# Date Author Comment
5134 10/01/2012 02:57 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonpath: Added back datasource_id, plantcode to make taxonpath datasource-specific again. This way, the original name components can still be stored in taxonpath, in addition to storing the concatenated name in a datasource-general taxonpath for use by TNRS.

5133 09/28/2012 03:46 PM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/map.csv: Mapped columns for components of original, submitted name

5132 09/28/2012 03:33 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv, VegCore.csv: Removed no longer used verbatimScientificNameWithAuthorship. Use scientificNameWithAuthorship instead, and map accepted (scrubbed) names to acceptedScientificNameWithAuthorship to create the canon_taxonpath_id link.

5131 09/28/2012 03:28 PM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/map.csv: Remapped to new accepted* taxonomic terms

5130 09/28/2012 03:23 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped accepted* taxonomic terms

5129 09/28/2012 03:00 PM Aaron Marcuse-Kubitza

sql_io.py: cleanup_table(): Don't clean up the pkey, because the canonicalization involved may produce collisions (as it does for TNRS.tnrs)

5128 09/28/2012 02:58 PM Aaron Marcuse-Kubitza

sql.py: Added pkey_col_()

5127 09/28/2012 02:31 PM Aaron Marcuse-Kubitza

tnrs.py: tnrs_request(): Added comment that names containing only whitespace characters are ignored by TNRS and do not receive a response row. Our tnrs_db and reimport pipeline handles the necessary re-matching-up by just creating taxonpaths for each Name_submitted, and then letting the data import process on the following import attach to the prepopulated taxonpaths.

5126 09/28/2012 02:17 PM Aaron Marcuse-Kubitza

tnrs_db: Exclude taxonomic names which have already been scrubbed, by using a filter-out LEFT JOIN on TNRS.tnrs

5125 09/28/2012 02:02 PM Aaron Marcuse-Kubitza

tnrs.py: max_pause: Changed to 30 min because TNRS sometimes freezes for ~10 min. The freezing usually happens while the data is being uploaded rather than when it's being retrieved, so that the max_pause would not apply, but to be on the safe side, requests should not time out unnecessarily.

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