Project

General

Profile

Statistics
| Revision:

# Date Author Comment
223 12/20/2011 05:42 PM Aaron Marcuse-Kubitza

Added auto-generated vegbien_empty.sql to empty the vegbien db

222 12/20/2011 04:55 PM Aaron Marcuse-Kubitza

Test output to VegBIEN instead of VegBank

221 12/20/2011 04:54 PM Aaron Marcuse-Kubitza

VegX-VegBIEN.organisms.csv: sort output of repl

220 12/20/2011 04:46 PM Aaron Marcuse-Kubitza

review: Added nullglob

219 12/20/2011 04:44 PM Aaron Marcuse-Kubitza

review: Don't process replacements spreadsheets

218 12/20/2011 04:44 PM Aaron Marcuse-Kubitza

Moved schema replacements from VegBank-VegBIEN.csv to VegBank-VegBIEN.schema.csv

217 12/20/2011 04:32 PM Aaron Marcuse-Kubitza

VegBank-VegBIEN.csv: Support PostgreSQL before 8.4

216 12/20/2011 04:29 PM Aaron Marcuse-Kubitza

repl: Added support for blank lines. Only add whole word regexp code to inputs w/o any regexp metachars.

215 12/20/2011 04:13 PM Aaron Marcuse-Kubitza

Create vegbien db from mappings/schemas/vegbien.sql

214 12/20/2011 04:12 PM Aaron Marcuse-Kubitza

VegBank-VegBIEN.csv: Added replacements for SQL create script conversion

213 12/20/2011 03:56 PM Aaron Marcuse-Kubitza

Generate vegbien db create SQL from vegbank.sql using repl

212 12/20/2011 03:55 PM Aaron Marcuse-Kubitza

Generate vegbien db create SQL from vegbank.sql using repl

211 12/20/2011 03:54 PM Aaron Marcuse-Kubitza

repl: Fixed bug in reading arguments

210 12/20/2011 03:38 PM Aaron Marcuse-Kubitza

repl: Don't add whole-word regexp for inputs that already have regexp metachars

209 12/20/2011 03:26 PM Aaron Marcuse-Kubitza

Removed mappings/VegBank-VegBIEN.organisms.csv because now using replacements spreadsheet

208 12/20/2011 03:24 PM Aaron Marcuse-Kubitza

mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet

207 12/20/2011 03:23 PM Aaron Marcuse-Kubitza

mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet

206 12/20/2011 03:23 PM Aaron Marcuse-Kubitza

mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet

205 12/20/2011 02:57 PM Aaron Marcuse-Kubitza

Added repl to perform replacements on a spreadsheet or file

204 12/20/2011 01:38 PM Aaron Marcuse-Kubitza

scripts/Makefile: removed extra test-% target

203 12/20/2011 01:38 PM Aaron Marcuse-Kubitza

README.TXT: Updated

202 12/20/2011 01:36 PM Aaron Marcuse-Kubitza

scripts/Makefile: install/uninstall targets

201 12/20/2011 01:36 PM Aaron Marcuse-Kubitza

bien_user_create: Print instructions in sequence with password prompts

200 12/19/2011 06:16 PM Aaron Marcuse-Kubitza

mappings to VegBIEN: Accounted for remaining ALTER TABLE statements

199 12/19/2011 05:48 PM Aaron Marcuse-Kubitza

Renamed format*_for_review to review and added for_review to make clean

198 12/19/2011 05:41 PM Aaron Marcuse-Kubitza

mappings: Added mappings to VegBIEN

197 12/19/2011 05:25 PM Aaron Marcuse-Kubitza

mappings/Makefile: Simplified

196 12/19/2011 05:22 PM Aaron Marcuse-Kubitza

mappings/Makefile: Simplified

195 12/19/2011 04:59 PM Aaron Marcuse-Kubitza

README.TXT: Updated

194 12/19/2011 04:47 PM Aaron Marcuse-Kubitza

Added vegbien DB admin scripts

193 12/16/2011 03:54 PM Aaron Marcuse-Kubitza

join_all_vegbank: Sort output by both columns

192 12/16/2011 03:48 PM Aaron Marcuse-Kubitza

mappings/VegX-VegBank.organisms.csv: Sorted by both columns

191 12/16/2011 03:48 PM Aaron Marcuse-Kubitza

mappings/Makefile: Sort VegBank-VegBIEN.organisms.csv by both columns

190 12/16/2011 03:47 PM Aaron Marcuse-Kubitza

extract_plot_map: Removed because functionality now in Makefile

189 12/16/2011 03:46 PM Aaron Marcuse-Kubitza

sort: Can sort on multiple columns

188 12/16/2011 03:17 PM Aaron Marcuse-Kubitza

Added basic VegX-VegBIEN mapping

187 12/16/2011 02:02 PM Aaron Marcuse-Kubitza

Added union and join_passthru

186 12/16/2011 02:02 PM Aaron Marcuse-Kubitza

env_password: Print Usage message to stderr

185 12/16/2011 01:29 PM Aaron Marcuse-Kubitza

test/map: Create output dir if it doesn't exist

184 12/16/2011 01:24 PM Aaron Marcuse-Kubitza

Converted scripts back to bash that required bash-specific features

183 12/16/2011 01:23 PM Aaron Marcuse-Kubitza

Converted scripts back to bash that required bash-specific features

182 12/16/2011 01:13 PM Aaron Marcuse-Kubitza

Fixed test/map to work with sh

181 12/16/2011 01:05 PM Aaron Marcuse-Kubitza

Replaced /bin/bash with /bin/sh

180 12/15/2011 04:16 PM Aaron Marcuse-Kubitza

join: Added usage item for repeated joins

179 12/15/2011 04:13 PM Aaron Marcuse-Kubitza

join: Changed order of args and redirects to be more intuitive

178 12/15/2011 04:09 PM Aaron Marcuse-Kubitza

Renamed ch_map_root to ch_root

177 12/15/2011 04:08 PM Aaron Marcuse-Kubitza

Renamed join_maps to join

176 12/15/2011 12:20 PM Aaron Marcuse-Kubitza

Merged test Makefile into main scripts Makefile

175 12/15/2011 12:05 PM Aaron Marcuse-Kubitza

test/map: Turn off test mode (don't run diff) when env var n (for # rows) is set

174 12/15/2011 11:39 AM Aaron Marcuse-Kubitza

Added SALVIAS DB mapping for plots data

173 12/15/2011 11:37 AM Aaron Marcuse-Kubitza

VegX-VegBank mapping: Fixed VegBank XPath for commName.commName field

172 12/15/2011 11:35 AM Aaron Marcuse-Kubitza

db_xml.py: Use pointer target's name as pointer type where possible. Emphasize that pointer type determined from the pointer name itself is a guess based on common database conventions.

171 12/15/2011 11:31 AM Aaron Marcuse-Kubitza

xpath.py: Changed backward (child-to-parent) pointer ID abbr expansion to happen in get() when source node's tag name is known. This deals with XPath elements that are '.' being used as a pointer source.

170 12/14/2011 05:31 PM Aaron Marcuse-Kubitza

xpath.py: Moved abbr expansion code to separate function

169 12/14/2011 04:41 PM Aaron Marcuse-Kubitza

test/map: Process all tables for a given DB (.sh) input

168 12/14/2011 03:26 PM Aaron Marcuse-Kubitza

Removed /'s from DB input mappings

167 12/14/2011 01:46 PM Aaron Marcuse-Kubitza

map: Use row's index instead of pkey as ID in XML output

166 12/14/2011 01:45 PM Aaron Marcuse-Kubitza

test/map: Compare via-VegX output to direct output

165 12/14/2011 01:13 PM Aaron Marcuse-Kubitza

xpath.py: Changed order that main and other branches are processed in so it is consistent with the order the branches are specified in the XPath

164 12/14/2011 12:03 PM Aaron Marcuse-Kubitza

map: Handle metadata in order with regular mappings

163 12/14/2011 11:33 AM Aaron Marcuse-Kubitza

Accepted VegBank test output for new CSV mapping order

162 12/14/2011 11:26 AM Aaron Marcuse-Kubitza

map: Changed CSV input to process mappings in the order they are in the spreadsheet, rather than the order of the CSV columns

161 12/13/2011 05:18 PM Aaron Marcuse-Kubitza

map: Added support for XML input

160 12/13/2011 05:17 PM Aaron Marcuse-Kubitza

Accepted new test output for sorted SALVIAS_db-VegBank mapping

159 12/13/2011 05:07 PM Aaron Marcuse-Kubitza

mappings to VegBank: Sorted by output column to help VegX-VegBank conversion put elements in the same order as source-VegBank

158 12/13/2011 04:57 PM Aaron Marcuse-Kubitza

join_all_vegbank: Updated to sort output maps

157 12/13/2011 04:57 PM Aaron Marcuse-Kubitza

Added script to sort a spreadsheet

156 12/13/2011 03:51 PM Aaron Marcuse-Kubitza

xpath.py: Allowed empty names in XPaths

155 12/13/2011 03:48 PM Aaron Marcuse-Kubitza

xpath.py: Added automatic conversion of strings to paths where needed.

154 12/13/2011 03:00 PM Aaron Marcuse-Kubitza

xpath.py: Added caching of parsed XPaths. Added automatic conversion of strings to paths where needed.

153 12/13/2011 02:59 PM Aaron Marcuse-Kubitza

Added str() method to XML nodes

152 12/13/2011 02:58 PM Aaron Marcuse-Kubitza

Fixed VegX-VegBank mapping syntax error

151 12/13/2011 02:17 PM Aaron Marcuse-Kubitza

Added faded beginning of string in Parser syntax errors

150 12/13/2011 02:01 PM Aaron Marcuse-Kubitza

Updated mappings Makefile

149 12/13/2011 02:00 PM Aaron Marcuse-Kubitza

Added Makefiles for scripts and test

148 12/13/2011 01:54 PM Aaron Marcuse-Kubitza

Added mappings Makefile

147 12/13/2011 12:28 PM Aaron Marcuse-Kubitza

Added human-readable SALVIAS_db mappings

146 12/13/2011 12:28 PM Aaron Marcuse-Kubitza

db_xml.get(): Pass limit through to SQL query

145 12/13/2011 11:48 AM Aaron Marcuse-Kubitza

Regenerated human-readable mappings

144 12/12/2011 05:39 PM Aaron Marcuse-Kubitza

Fixed documentation for xml_funcs

143 12/12/2011 05:38 PM Aaron Marcuse-Kubitza

Refactored xml_dom.set_value() to avoid needing a doc parameter for the XML document

142 12/12/2011 05:35 PM Aaron Marcuse-Kubitza

xpath.py: Refactored xml_func.py to avoid needing a doc parameter for the XML document

141 12/12/2011 05:30 PM Aaron Marcuse-Kubitza

xpath.py: Refactored to avoid needing a doc parameter for the XML document

140 12/12/2011 04:41 PM Aaron Marcuse-Kubitza

Fixed DB input to ignore NULL values

139 12/12/2011 04:27 PM Aaron Marcuse-Kubitza

xml_dom.py: Changed all uses of name_of(node) to node.tagName

138 12/12/2011 04:23 PM Aaron Marcuse-Kubitza

Made XML node names case-sensitive

137 12/12/2011 04:20 PM Aaron Marcuse-Kubitza

mappings to VegBank: Fixed incorrect mappings found after disabling heuristic search for missing fields

136 12/12/2011 03:49 PM Aaron Marcuse-Kubitza

test/map: Ignore diff exit status

135 12/12/2011 03:34 PM Aaron Marcuse-Kubitza

map: Implemented DB input support for querying a single table

134 12/09/2011 05:36 PM Aaron Marcuse-Kubitza

Added SALVIAS_db test accepted output

133 12/09/2011 05:35 PM Aaron Marcuse-Kubitza

map: Continued to add DB input support

132 12/09/2011 04:54 PM Aaron Marcuse-Kubitza

test/map: Echo command used to import db config

131 12/09/2011 04:02 PM Aaron Marcuse-Kubitza

Added support for multiple database engines. Changed SALVIAS_db input to use user-entered password.

130 12/09/2011 01:58 PM Aaron Marcuse-Kubitza

map: Allow db config vars to be optional. SALVIAS_db test: Changed to use salvias_plots and XPath mapping syntax.

129 12/09/2011 01:32 PM Aaron Marcuse-Kubitza

Renamed SALVIAS_db test input to use organisms table

128 12/09/2011 01:29 PM Aaron Marcuse-Kubitza

Re-committed accepted_outputs

127 12/09/2011 01:23 PM Aaron Marcuse-Kubitza

Renamed test/map output to remove CSV/DB indicator because that is now specified in the datasource name

126 12/09/2011 01:18 PM Aaron Marcuse-Kubitza

map: Started adding database get by XPath functionality

125 12/08/2011 06:48 PM Aaron Marcuse-Kubitza

format_for_review: Fixed bug where Comments column would be reformatted in addition to mappings columns

124 12/08/2011 05:35 PM Aaron Marcuse-Kubitza

Regenerated human-readable mappings