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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 5837 about 12 years Aaron Marcuse-Kubitza tnrs_db: Fetching names to scrub: Omit sql.sele...
  config 272 about 13 years Aaron Marcuse-Kubitza Moved bien_password to new config dir
  inputs 5835 about 12 years Aaron Marcuse-Kubitza inputs/.NCBI/nodes/create.sql: Make genus compl...
  lib 5827 about 12 years Aaron Marcuse-Kubitza sql_io.py: put_table(): ensure_cond(): Fixed bu...
  mappings 5833 about 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: matched taxonlabe...
  schemas 5838 about 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: analytical_db_view: dataso...
  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 9.87 KB 5679 about 12 years Aaron Marcuse-Kubitza root Makefile: VegBIEN DB: Schemas: schemas/rot...
README.TXT 12.9 KB 5802 about 12 years Aaron Marcuse-Kubitza README.TXT: Generate the local TNRS cache from ...
map 989 Bytes 5158 about 12 years Aaron Marcuse-Kubitza root map: Removed no longer needed public schem...
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
5838 10/30/2012 04:19 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_db_view: datasource table: Fixed bug where need to filter by creator_id = party_id in order to use just root parties (datasources)

5837 10/30/2012 03:40 AM Aaron Marcuse-Kubitza

tnrs_db: Fetching names to scrub: Omit sql.select() fields param because it will be filled in with its default value

5836 10/30/2012 03:29 AM Aaron Marcuse-Kubitza

import_all: Pass command-line args (such as make vars) to all commands, not just with_all, so that a custom public schema is properly used by all commands

5835 10/30/2012 02:57 AM Aaron Marcuse-Kubitza

inputs/.NCBI/nodes/create.sql: Make genus completely globally unique by removing duplicates. Note that only duplicates with ranks at or below the genus level need be removed, which for this dataset is just genus and subgenus.

5834 10/30/2012 02:00 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel: taxonlabel_required_key constraint: Also allow taxonlabels with just a sourceaccessioncode, to support looking up parent taxonlabels using just their sourceaccessioncode (e.g. in NCBI)

5833 10/30/2012 01:23 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: matched taxonlabel: Don't include taxonName in the concatenated taxonomicname. This also prevents the creation of the matched taxonlabel entirely when only the taxonName is provided.

5832 10/30/2012 01:20 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Don't create matched taxonlabel if taxonName was provided. This fixes a bug where an NCBI node was incorrectly pointing to a TNRS name, when the reference should only be the other way around. This may also fix the TNRS slowdown, if it was caused by circular matched_label_id references.

5831 10/30/2012 12:47 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel_2_set_canon_label_id_on_insert(): Fixed bug where also need to set canon_label_id based on matched_label_id here, not just in taxonlabel_2_set_canon_label_id_on_update(), because the matched_label_id could be specified when the taxonlabel is first created

5830 10/30/2012 12:34 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel_2_set_canon_label_id_on_*(): Fixed bug where need to use := instead of = to perform assignment of canon_label_id

5829 10/30/2012 12:17 AM Aaron Marcuse-Kubitza

schemas/tree_cross-links.sql: Updated for schema changes

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