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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 5787 about 12 years Aaron Marcuse-Kubitza tnrs_db: Making TNRS request: Fixed bug where n...
  config 272 about 13 years Aaron Marcuse-Kubitza Moved bien_password to new config dir
  inputs 5825 about 12 years Aaron Marcuse-Kubitza inputs/import.stats.xls: Updated import times. ...
  lib 5827 about 12 years Aaron Marcuse-Kubitza sql_io.py: put_table(): ensure_cond(): Fixed bu...
  mappings 5790 about 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: Only prepend the ...
  schemas 5830 about 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: taxonlabel_2_set_canon_lab...
  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
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.

5824 10/29/2012 09:37 PM Aaron Marcuse-Kubitza

sql_io.py: put_table(): Assertion that into and full_in_table have the same row count: Allow into to have more rows than full_in_table, in case an input row matched multiple output rows. This should not happen for a properly-configured database, but seems to happen periodically nevertheless (currently, to the MO datasource) and should not abort the import when it does.

5823 10/26/2012 08:18 PM Aaron Marcuse-Kubitza

sql.py: parse_exception(): "could not create unique index" DuplicateKeyException: Fixed bug where can't use make_DuplicateKeyException() because it tries to retrieve information about the index in question, but the index it was trying to create doesn't exist

5822 10/26/2012 08:10 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_db_view: Renamed datasource's taxonverbatim to datasource_taxonverbatim to distinguish it from the other taxonverbatims that are joined on (parsed_taxonverbatim, accepted_taxonverbatim)

5821 10/26/2012 07:18 PM Aaron Marcuse-Kubitza

inputs/.NCBI/nodes/create.sql: Make genus (mostly) globally unique by removing kingdom Animalia, which has significant genus overlap with plants. This reduces the number of duplicated genera from 578 to 65 (determined with `SELECT name_txt, count(), array_agg(rank) FROM "NCBI".nodes GROUP BY name_txt HAVING count() > 1 AND 'genus' = ALL (array_agg(rank))`).

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