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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 4751 about 12 years Aaron Marcuse-Kubitza backups/Makefile: Backups: Full DB: Specify the...
  bin 5787 about 12 years Aaron Marcuse-Kubitza tnrs_db: Making TNRS request: Fixed bug where n...
  config 272 almost 13 years Aaron Marcuse-Kubitza Moved bien_password to new config dir
  inputs 5834 about 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: taxonlabel: taxonlabel_req...
  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 5834 about 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: taxonlabel: taxonlabel_req...
  to_do 4524 about 12 years Aaron Marcuse-Kubitza to_do/timeline.doc: Updated to reflect addition...
  validation 4523 about 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 about 12 years Aaron Marcuse-Kubitza Regenerated root unmapped_terms.csv, new_terms.csv
unmapped_terms.csv 5.8 KB 4887 about 12 years Aaron Marcuse-Kubitza Regenerated root unmapped_terms.csv, new_terms.csv

Latest revisions

# Date Author Comment
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

5828 10/30/2012 12:16 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel_update_ancestors(): Include ancestors for both parent_id and matched_label_id rather than just one or the other. This avoids needing to delete existing ancestors for the parent_id when a matched_label_id is added and overrides it. This should reduce the TNRS import time if the slowdown was due to the need to delete parent_id ancestors when later adding a matched_label_id (which only occurs in a separate step in the TNRS datasource).

5827 10/30/2012 12:07 AM Aaron Marcuse-Kubitza

sql_io.py: put_table(): ensure_cond(): Fixed bug where test if any rows failed cond did not check if cur != None (which is the case when cond == sql_gen.true_expr) before checking cur.rowcount

5826 10/29/2012 10:26 PM Aaron Marcuse-Kubitza

sql_gen.py: simplify_expr(): Don't require () around NULL IS NULL and NULL IS NOT NULL because extra parentheses are not provided in index conditions, only in check constraint conditions

5825 10/29/2012 10:06 PM Aaron Marcuse-Kubitza

inputs/import.stats.xls: Updated import times. The TNRS import has slowed down significantly, possibly due to a bug in the autopopulation of the taxonlabel_relationship table when the input data contains cycles.

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