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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 5672 about 12 years Aaron Marcuse-Kubitza pg_dump_vegbien: Added opts env var to allow sp...
  config 272 about 13 years Aaron Marcuse-Kubitza Moved bien_password to new config dir
  inputs 5727 about 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: _is_higher_taxon(...
  lib 5726 about 12 years Aaron Marcuse-Kubitza sql_io.py: put_table(): is_function: Moved defi...
  mappings 5727 about 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: _is_higher_taxon(...
  schemas 5705 about 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: taxonlabel: taxonlabel_2_s...
  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 13 KB 5684 about 12 years Aaron Marcuse-Kubitza README.TXT: Documentation: To import and scrub ...
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
5727 10/23/2012 08:01 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: _is_higher_taxon() calls: Default to true if the rank can't be parsed to a taxonrank enum value

5726 10/23/2012 07:56 AM Aaron Marcuse-Kubitza

sql_io.py: put_table(): is_function: Moved definition of wrapper function inside try block of main loop because the creation of the empty pkeys table (whose row type is needed for the wrapper function) can itself produce MissingCastExceptions, which must be thrown inside the loop in order to be handled properly

5725 10/23/2012 07:05 AM Aaron Marcuse-Kubitza

db_xml.py: put(): Indicate no parent_ids_loc using no_parent_ids_loc sentinel instead of None to support parent_ids_locs that are equal to None (e.g. if the parent node had an error). Always forward parent_ids_loc to children with fkeys to parent, even on error, because the parent table may not be required for the child tables to be valid, such as for taxonomic-data-only datasets that nevertheless have nodes for the non-taxonomic tables in their mappings.

5724 10/23/2012 06:38 AM Aaron Marcuse-Kubitza

sql.py: parse_exception(): types cannot be matched MissingCastException: Use the first type as the type to cast to instead of text

5723 10/23/2012 05:59 AM Aaron Marcuse-Kubitza

sql.py: parse_exception(): InvalidValueException: Fixed bug in regexp where can't use .*? before (?:...)? surrounding matched value, because it prevents the value from being matched now that it is optional

5722 10/23/2012 05:52 AM Aaron Marcuse-Kubitza

inputs/.NCBI/nodes/header.csv: Updated for new staging table format, which includes a row_num column in each joined table

5721 10/23/2012 05:51 AM Aaron Marcuse-Kubitza

inputs/.NCBI/nodes/create.sql: Updated for new src table names

5720 10/23/2012 05:36 AM Aaron Marcuse-Kubitza

xml_func.py: process(): Pass on_error through to sql_io.put(). This fixes a bug in row-based import where DB errors in the xml_func.process() phase would abort the entire import instead of being tracked and having the return value set to None.

5719 10/23/2012 05:33 AM Aaron Marcuse-Kubitza

sql_io.py: put(): Pass on_error through to put_table()

5718 10/23/2012 05:19 AM Aaron Marcuse-Kubitza

sql_io.py: put_table(): log_exc(): Return False if removing all rows and have callers break the main loop so that no further exception-handling code is processed before the main loop is exited

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