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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 5821 about 12 years Aaron Marcuse-Kubitza inputs/.NCBI/nodes/create.sql: Make genus (most...
  lib 5824 about 12 years Aaron Marcuse-Kubitza sql_io.py: put_table(): Assertion that into and...
  mappings 5790 about 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: Only prepend the ...
  schemas 5822 about 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: analytical_db_view: Rename...
  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
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))`).

5820 10/26/2012 07:08 PM Aaron Marcuse-Kubitza

inputs/.NCBI/nodes/create.sql: Added foreign key on parent tax_id with covering index

5819 10/26/2012 07:06 PM Aaron Marcuse-Kubitza

input.Makefile: Staging tables installation: Added %/uninstall, %/reinstall to allow reinstalling individual tables

5818 10/26/2012 06:00 PM Aaron Marcuse-Kubitza

sql_io.py: put_table(): ensure_cond(): When adding the failed condition to the errors table, also include the original, untranslated condition from the DB schema in addition to the translation of the condition into the input schema

5817 10/26/2012 05:45 PM Aaron Marcuse-Kubitza

sql_io.py: track_data_error(): Fixed bug where errors whose column had no srcs (indicated by () ) were incorrectly being ignored. This affected NOT NULL exceptions where the column was not provided by the dataset.

5816 10/26/2012 05:38 PM Aaron Marcuse-Kubitza

sql_gen.py: If no cols had srcs, return [] instead of the [()] that itertools.product() would have returned

5815 10/26/2012 05:38 PM Aaron Marcuse-Kubitza

sql_io.py: track_data_error(): Support errors with no columns by inserting a single entry with column set to NULL

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