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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 7037 almost 12 years Aaron Marcuse-Kubitza backups/Makefile: Synchronization: %/download: ...
  bin 7148 almost 12 years Aaron Marcuse-Kubitza bin/map: map_table(): Resolving prefixes: Fixed...
  config 6321 about 12 years Aaron Marcuse-Kubitza Added config/bien_read_password
  inputs 7151 almost 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: Use new TNRS.tnrs_canon in...
  lib 7141 almost 12 years Aaron Marcuse-Kubitza xml_func.py: Simplifying functions: Merging: Ad...
  mappings 7150 almost 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: "if has verbatim ...
  schemas 7151 almost 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: Use new TNRS.tnrs_canon in...
  to_do 4524 over 12 years Aaron Marcuse-Kubitza to_do/timeline.doc: Updated to reflect addition...
  validation 5971 about 12 years Aaron Marcuse-Kubitza Updated validation/BIEN2_Analytical_DB_overview...
Makefile 11.3 KB 7082 almost 12 years Aaron Marcuse-Kubitza root Makefile: Removed $(subMake), which is now...
README.TXT 16.5 KB 7122 almost 12 years Aaron Marcuse-Kubitza bin/map: Made $redo flag default to off, becaus...
map 1001 Bytes 6949 about 12 years Aaron Marcuse-Kubitza vegbien_dest: Changed default $prefix to "", so...
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
7151 01/10/2013 11:12 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Use new TNRS.tnrs_canon instead of tnrs+accepted to avoid creating additional taxonlabels for the parsed, matched, and accepted names and instead just use the most-canonicalized name of the names output by TNRS (the accepted name if available, or the matched name otherwise)

7150 01/10/2013 10:50 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: "if has verbatim name" _if statements that filter something out for TNRS mappings: Also assume true if taxonIsCanonical is specified, because some TNRS tables (eventually such as public.unscrubbed_taxondetermination_view) do not specify a separate "verbatim" taxondetermination but do provide taxonIsCanonical as a flag to turn various mappings on and off

7149 01/10/2013 09:06 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Remapped matched*Fit_fraction to taxondetermination.taxonfit when a taxondetermination, not just a taxonlabel, is provided

7148 01/10/2013 09:03 PM Aaron Marcuse-Kubitza

bin/map: map_table(): Resolving prefixes: Fixed bug where need to use list instead of tuple for metadata value mappings

7147 01/10/2013 08:16 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxondetermination: Added CHECK constraint to allow only taxondeterminations with a minimum fit fraction of 80%, analogous to taxonlabel's taxonlabel_1_matched_label_min_fit() trigger

7146 01/09/2013 05:34 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Don't create a separate TNRS input taxonlabel if taxonIsCanonical exists

7145 01/09/2013 05:24 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_canon: Fixed bug where need to always use Unmatched_terms from tnrs rather than tnrs_accepted

7144 01/09/2013 05:07 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: Added tnrs_canon, which stores the most canonicalized name output by TNRS

7143 01/09/2013 04:17 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: accepted_taxonverbatim: Fixed bug where need to join only to the taxonverbatim whose morphospecies is NULL, to avoid joining to multiple taxonverbatims at once. This extra filter is now needed because there can be multiple taxonverbatims for a taxonlabel with different morphospecies.

7142 01/09/2013 03:59 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonlabel.taxonomicname: Prepend the family to the rest of the name using new _merge_prefix() instead of _join_words()/_nullIf(), so that any input taxonomic name that includes the family will not have the family duplicated in the combined taxonomic name. Previously, the duplication was removed only when the rest of the input name was equal to the family. This change fixes a bug in the new TNRS import where a pre-concatenated taxonomic name (Accepted_scientific_name) which includes the family is now used instead of Accepted_name, which only includes it when it's equal to the family.

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