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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 over 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 5803 over 12 years Aaron Marcuse-Kubitza inputs/.TNRS/tnrs/map.csv: Added _nullIf filter...
  lib 5792 over 12 years Aaron Marcuse-Kubitza sql.py: parse_exception(): function MissingCast...
  mappings 5790 over 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: Only prepend the ...
  schemas 5789 over 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: Added _taxon_family_requir...
  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 over 12 years Aaron Marcuse-Kubitza root Makefile: VegBIEN DB: Schemas: schemas/rot...
README.TXT 12.9 KB 5802 over 12 years Aaron Marcuse-Kubitza README.TXT: Generate the local TNRS cache from ...
map 989 Bytes 5158 over 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
5803 10/26/2012 03:42 PM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/map.csv: Added _nullIf filter to remove "Unknown" values for Accepted_name_family

5802 10/26/2012 03:35 PM Aaron Marcuse-Kubitza

README.TXT: Generate the local TNRS cache from the test_taxonomic_names rather than syncing it with the vegbiendev TNRS cache, so that the automated test's inserted row count stays the same regardless of the contents of the full-DB TNRS cache

5801 10/26/2012 03:34 PM Aaron Marcuse-Kubitza

README.TXT: Backups: Added TNRS cache section

5800 10/26/2012 03:12 PM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/test.xml.ref: Accepted inserted row count using TNRS cache created from test_taxonomic_names. Using a standard set of names for the test ensures that the inserted row count will not change when the full-DB TNRS cache changes.

5799 10/26/2012 02:48 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_accepted_names: Prepend the Accepted_name_family to the taxonomic name that will be submitted back to TNRS for parsing, because TNRS input names now always include the family when it's provided

5798 10/26/2012 02:46 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_accepted_names: Use simpler array_to_string() instead of || and COALESCE to put together the taxonomic name that will be submitted back to TNRS for parsing. Note that this requires defining an IMMUTABLE wrapper function for array_to_string(), because pg_catalog.array_to_string() is declared STABLE but indexes require functions to be IMMUTABLE (http://www.mail-archive.com/pgsql-hackers@postgresql.org/msg156323.html).

5797 10/26/2012 02:42 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: Don't hardcode the schema name

5796 10/26/2012 02:40 PM Aaron Marcuse-Kubitza

input.Makefile: Staging tables installation: sql/install: Provide the datasource's schema to the script in :schema, so it can refer to its own elements explicitly when it's not possible to rely on the search_path. This is the case for functions that have the same signature as (and are intended to replace) a pg_catalog function, because the pg_catalog function will be used in preference to the datasource function regardless of the search_path.

5795 10/26/2012 02:06 PM Aaron Marcuse-Kubitza

input.Makefile: Staging tables installation: $(cleanup): If a cleanup.sql is provided, only run it and don't do default cleanup, to allow tables to override rather than just add to default cleanup operations. This prevents the automatic replacement of certain strings (sql_io.null_strs) with NULL on TNRS, and keeps the TNRS cache mostly as it was output by the TNRS service. Note that empty strings are still replaced with NULL by COPY FROM in sql_io.append_csv(). This is necessary for TNRS import to work properly, because although '' generally means NULL, it is not treated that way by PostgreSQL.

5794 10/26/2012 01:53 PM Aaron Marcuse-Kubitza

input.Makefile: Staging tables installation: Moved custom cleanup.sql cleanup operations to main $(cleanup) function, so custom cleanup operations would run whenever any target (such as %/install) invokes $(cleanup), not just manually through %/cleanup

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