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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 6965 almost 12 years Aaron Marcuse-Kubitza backups/Makefile: Factored $(isMac) out into li...
  bin 6981 almost 12 years Aaron Marcuse-Kubitza make_analytical_db: Automatically call export_a...
  config 6321 about 12 years Aaron Marcuse-Kubitza Added config/bien_read_password
  inputs 6950 almost 12 years Aaron Marcuse-Kubitza vegbien_dest callers: Removed no longer needed ...
  lib 6978 almost 12 years Aaron Marcuse-Kubitza lib/common.Makefile: $(confirm): Added comment ...
  mappings 6893 almost 12 years Aaron Marcuse-Kubitza mappings/Makefile: VegCore.csv: Filter out the ...
  schemas 6982 almost 12 years Aaron Marcuse-Kubitza schemas/Makefile: Use $* instead of $(@D) for c...
  to_do 4524 about 12 years Aaron Marcuse-Kubitza to_do/timeline.doc: Updated to reflect addition...
  validation 5971 about 12 years Aaron Marcuse-Kubitza Updated validation/BIEN2_Analytical_DB_overview...
Makefile 11.4 KB 6916 almost 12 years Aaron Marcuse-Kubitza Moved schemas-related commands from root Makefi...
README.TXT 16.1 KB 6977 almost 12 years Aaron Marcuse-Kubitza import_all: after_import(): Added `make backups...
map 1001 Bytes 6949 almost 12 years Aaron Marcuse-Kubitza vegbien_dest: Changed default $prefix to "", so...
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
6982 12/20/2012 11:21 AM Aaron Marcuse-Kubitza

schemas/Makefile: Use $* instead of $(@D) for clarity. $(@D) is only needed when the dir part of the target includes a prefix in addition to the % stem.

6981 12/20/2012 10:45 AM Aaron Marcuse-Kubitza

make_analytical_db: Automatically call export_analytical_db when finished

6980 12/20/2012 10:35 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: make_family_higher_plant_group(): Added `taxonepithet IS NOT NULL` filter, to allow make_analytical_db to proceed even when the NCBI import fails (leaving some nodes with rank = 'family' but no associated taxonepithet). The most recent NCBI import failed due to the search_path/DuplicateException bug resulting from the import schema and public being in the search_path together.

6979 12/20/2012 10:14 AM Aaron Marcuse-Kubitza

schemas/Makefile: Fixed bug where need `SHELL := /bin/bash` for \$(confirmRmPublicSchema) to work correctly

6978 12/20/2012 10:12 AM Aaron Marcuse-Kubitza

lib/common.Makefile: $(confirm): Added comment that this requires `SHELL := /bin/bash` to work correctly

6977 12/20/2012 10:09 AM Aaron Marcuse-Kubitza

import_all: after_import(): Added `make backups/vegbien.$version.backup/test`

6976 12/20/2012 10:05 AM Aaron Marcuse-Kubitza

sql.py: DbConn._db(): search_path: Don't append the existing search_path, because it usually includes the public schema, which is now different from the schema being imported into. This fixes a bug where sql.function_exists() would find public-schema functions in both the public schema and the import's schema because both were in the search_path, causing a DuplicateException "more than one function named ...". Note that the elements of the existing search_path are no longer needed now that vegbien_dest's $schemas includes $public. Also note that if an instance of DbConn does not specify the schemas param, the existing search_path will be left as-is rather than overwritten with an empty list.

6975 12/20/2012 09:54 AM Aaron Marcuse-Kubitza

README.TXT: Data import: recording the import times in inputs/import.stats.xls: Added step to determine the import date using import_date

6974 12/20/2012 09:52 AM Aaron Marcuse-Kubitza

import_date: Added note that Mac and Linux differ in the order they sort the logs in

6973 12/20/2012 09:50 AM Aaron Marcuse-Kubitza

README.TXT: Data import: recording the import times in inputs/import.stats.xls: Updated pattern for new log filename format

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