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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 5523 about 12 years Aaron Marcuse-Kubitza sql.select() calls: Removed order_by=None every...
  config 272 about 13 years Aaron Marcuse-Kubitza Moved bien_password to new config dir
  inputs 5543 about 12 years Aaron Marcuse-Kubitza inputs/Madidi/Organism/map.csv: Total height: R...
  lib 5552 about 12 years Aaron Marcuse-Kubitza sql_gen.py: concat(): Allow multiple "column" s...
  mappings 5540 about 12 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: Mapped height_m
  schemas 5551 about 12 years Aaron Marcuse-Kubitza schemas/vegbien.sql: taxonconcept: taxonconcept...
  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 9.86 KB 5459 about 12 years Aaron Marcuse-Kubitza Makefile: Moved setting of $(root) before inclu...
README.TXT 12.9 KB 5519 about 12 years Aaron Marcuse-Kubitza README.TXT: Data import: On local machine: Adde...
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
5552 10/16/2012 09:18 PM Aaron Marcuse-Kubitza

sql_gen.py: concat(): Allow multiple "column" suffixes with "." when matching the existing suffix

5551 10/16/2012 08:47 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept: taxonconcept_update_ancestors() trigger: Corrected comment explaining why we don't need an ON DELETE trigger to say that this is because the foreign key for taxonconcept_ancestor.ancestor_id, not taxonconcept.parent_id, is ON DELETE CASCADE. The auto-deletion will also occur if taxonconcept.parent_id is ON DELETE CASCADE, because taxonconcept_ancestor.taxonconcept_id is ON DELETE CASCADE, but it is not actually necessary to have cascading deletes on taxonconcept.parent_id (and SET NULL may in fact sometimes be more appropriate).

5550 10/16/2012 08:33 PM Aaron Marcuse-Kubitza

schemas/tree_cross-links.sql: Removed header comments added by pgAdmin

5549 10/16/2012 08:30 PM Aaron Marcuse-Kubitza

schemas/tree_cross-links.sql: Updated for new taxonconcept_update_ancestors() trigger

5548 10/16/2012 08:21 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept: Rewrote taxonconcept() trigger to avoid completely reinserting the taxonconcept_ancestor entries of all descendants every time taxonconcept changes or using trigger recursion to find descendants. Instead, just delete the old parent's ancestors from and add the new parent's ancestors to each descendant, using taxonconcept_ancestor itself (with the new taxonconcept_ancestor_descendants index) to find all descendants. As an additional optimization, only update taxonconcept_ancestor if the parent_id or matched_concept_id has actually changed. This fixes a bug in NCBI where inserting taxonconcepts out of dependency order caused taxonconcept_ancestor entries to be repeatedly regenerated, slowing the import down to a crawl.

5547 10/16/2012 07:42 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept: Added taxonconcept_3_parent_id_avoid_self_ref() trigger to avoid recursive references in root taxonconcepts (taxonconcepts with no parent). This will simplify the new taxonconcept_update_ancestors() trigger.

5546 10/16/2012 06:32 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept_ancestor: Added taxonconcept_ancestor_descendants index to support looking up all the descendants for a taxonconcept. This will be used by the new taxonconcept_update_ancestors() trigger, which will support inserting taxonconcepts out of dependency order (such as for NCBI).

5545 10/16/2012 04:35 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: *_update_ancestors(): Made trigger deferred, so that it would run after all rows have been inserted in a bulk insert, such as during column-based import. This ensures that ancestors lists are not populated until all parents are inserted, which may occur out of order for datasources (such as NCBI) whose nodes are not in dependency order. (A node that newly acquires a parent will have to update all its descendants, which will then be updated again when its parent acquires its own parent.)

5544 10/16/2012 04:28 PM Aaron Marcuse-Kubitza

lib/PostgreSQL-MySQL.csv: Also filter out constraint triggers in addition to regular triggers

5543 10/15/2012 05:37 PM Aaron Marcuse-Kubitza

inputs/Madidi/Organism/map.csv: Total height: Remapped to height_m, assuming units based on the range and precision of values

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