[phylr] r43 commited - added comments

[codesite...@google.com]

Revision: 43
Author: dazhi.jiao
Date: Mon Jul 27 09:54:16 2009
Log: added comments
http://code.google.com/p/phylr/source/detail?r=43

Modified:
/trunk/phylr-gsoc/src/main/sql/TreeBaseBioSQLMig.sql

=======================================
--- /trunk/phylr-gsoc/src/main/sql/TreeBaseBioSQLMig.sql Sat Jul 25
12:43:15 2009
+++ /trunk/phylr-gsoc/src/main/sql/TreeBaseBioSQLMig.sql Mon Jul 27
09:54:16 2009
@@ -1,3 +1,31 @@
+-- This script is used to migrate TreeBase database to a BioSQL database
on PostgreSQL 8.3
+-- Please follow these steps before running this
+-- 1. create database
+-- # createdb biosql
+
+-- 2. import treebase dump (which I obtained from Bill Piel) into the
database
+-- # psql biosql < phylodb.sql
+
+-- 3. create biosql tables using the schema
+-- # psql biosql < biosqldb-pg.sql
+
+-- 4. Because both treebase and biosql phylodb extension have a table
name "node_path",
+-- so one of them needs to be renamed.
+-- open biosql-phylodb-pg.sql in a text editor, and rename "node_path"
to "bs_node_path".
+-- (Please note you have to use "bs_node_path", as it'll be referred in
this script!)
+
+-- 5. Create tables in the biosql-phylodb extension
+-- # psql biosql < biosql-phylodb-pg.sql
+
+-- 6. Now import the ncbi taxonomy using the biosql import script. Please
follow the biosql
+-- installation instructions for this step. If you already have BioPerl,
and BioPerlDB > 1.5.2,
+-- Then you can simply execute the following (The load_ncbi_taxonomy.pl)
is in the biosql
+-- distribution:
+-- # load_ncbi_taxonomy.pl --driver Pg --download yes --dbname biosql
+
+-- 8. Finally, execute this migration script
+-- # psql biosql < TreeBaseBioSQLMig.sql
+
ALTER TABLE tree ALTER COLUMN node_id DROP NOT NULL;
ALTER TABLE tree ALTER COLUMN name TYPE character varying(255);
ALTER TABLE tree ALTER COLUMN name DROP NOT NULL;
@@ -86,6 +114,7 @@
-- DROP TreeBase Tables
DROP TABLE edges, ncbi_names, ncbi_node_path, ncbi_nodes, node_path,
nodes, study, taxa, taxon_variants, trees;

+-- Rename table node_path back
ALTER TABLE bs_node_path RENAME TO node_path;