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# Date Author Comment
277 12/22/2011 07:29 PM Aaron Marcuse-Kubitza

psql_vegbien: Fixed comment to vegbien instead of vegbank

276 12/22/2011 07:11 PM Aaron Marcuse-Kubitza

psql_vegbien: Use new location of bien_password

275 12/22/2011 07:05 PM Aaron Marcuse-Kubitza

Makefile: Fixed paths to mappings dir for new scripts dir location

274 12/22/2011 07:02 PM Aaron Marcuse-Kubitza

Renamed util to bin

273 12/22/2011 06:59 PM Aaron Marcuse-Kubitza

Moved inputs_Makefile to inputs/input.Makefile

272 12/22/2011 06:55 PM Aaron Marcuse-Kubitza

Moved bien_password to new config dir

271 12/22/2011 06:52 PM Aaron Marcuse-Kubitza

Moved sample inputs to test dir

270 12/22/2011 06:42 PM Aaron Marcuse-Kubitza

Added symlink from scripts to new scripts destination

269 12/22/2011 06:40 PM Aaron Marcuse-Kubitza

Removed now-empty scripts dir

268 12/22/2011 06:39 PM Aaron Marcuse-Kubitza

Moved everything in scripts to root. inputs_Makefile: Don't run "all" when installing.

267 12/22/2011 06:24 PM Aaron Marcuse-Kubitza

Renamed bien_map to map

266 12/22/2011 06:22 PM Aaron Marcuse-Kubitza

Moved map to util

265 12/22/2011 06:14 PM Aaron Marcuse-Kubitza

fix_permissions: Don't chmod symlinks

264 12/22/2011 06:00 PM Aaron Marcuse-Kubitza

inputs_Makefile: Auto-generate map to VegBIEN and import data into vegbien from input DB

263 12/22/2011 05:59 PM Aaron Marcuse-Kubitza

inputs/SALVIAS: maps to VegX and VegBIEN

262 12/22/2011 05:58 PM Aaron Marcuse-Kubitza

bien_map: Runs map with BIEN defaults

261 12/22/2011 05:56 PM Aaron Marcuse-Kubitza

join_sort: Sorts a join on the output col

260 12/22/2011 03:20 PM Aaron Marcuse-Kubitza

inputs_Makefile: Require dbEngine var instead of defaulting to MySQL

259 12/22/2011 02:22 PM Aaron Marcuse-Kubitza

Moved inputs into svn

258 12/22/2011 01:46 PM Aaron Marcuse-Kubitza

Moved pre-BIEN 3 files into _archive folder

257 12/22/2011 01:46 PM Aaron Marcuse-Kubitza

test/map: Use db.sh syntax in *.sh tests

256 12/22/2011 01:45 PM Aaron Marcuse-Kubitza

inputs_Makefile: Generate db.sh with DB access info

255 12/22/2011 12:59 PM Aaron Marcuse-Kubitza

inputs_Makefile: Changed GRANT ALL to GRANT SELECT. Added REVOKE ALL. Added $(db).sql as prerequisite of install in case it needs to be auto-generated.

254 12/22/2011 12:30 PM Aaron Marcuse-Kubitza

scripts/Makefile: Added action for postgres-Darwin target

253 12/22/2011 12:11 PM Aaron Marcuse-Kubitza

scripts/Makefile: Added postgresql to postgres-Linux apt-get packages

252 12/21/2011 08:23 PM Aaron Marcuse-Kubitza

test/map: Changed to work on both nimoy and vegbiendev by selecting the appropriate MySQL user and password

251 12/21/2011 08:22 PM Aaron Marcuse-Kubitza

env_password: Added optional message arg

250 12/21/2011 07:47 PM Aaron Marcuse-Kubitza

Added uninstallation of inputs to Makefiles

249 12/21/2011 07:15 PM Aaron Marcuse-Kubitza

scripts/Makefile: Create bien user w/o prompting for password. Fixed syntax error.

248 12/21/2011 07:06 PM Aaron Marcuse-Kubitza

scripts/Makefile: Fixed syntax error

247 12/21/2011 07:03 PM Aaron Marcuse-Kubitza

Inputs now include inputs_Makefile to get mysql command, etc.

246 12/21/2011 06:30 PM Aaron Marcuse-Kubitza

scripts/Makefile: Use bien MySQL user for installing inputs

245 12/21/2011 06:26 PM Aaron Marcuse-Kubitza

scripts/Makefile: Use root MySQL user for creating bien user

244 12/21/2011 05:53 PM Aaron Marcuse-Kubitza

scripts/Makefile: Don't use root as MySQL admin user. Removed no-longer-needed sub-makes for setting DB login vars.

243 12/21/2011 05:10 PM Aaron Marcuse-Kubitza

Changed vegbien_dest and users of it to use separate bien_password file

242 12/21/2011 04:55 PM Aaron Marcuse-Kubitza

fix_permissions: Extend all user permissions to group

241 12/21/2011 04:26 PM Aaron Marcuse-Kubitza

scripts/Makefile: Added inputs

240 12/21/2011 03:24 PM Aaron Marcuse-Kubitza

mappings/Makefile: Cleaned up

239 12/21/2011 03:02 PM Aaron Marcuse-Kubitza

fix_permissions: Don't add group write perms to read-only files

238 12/21/2011 01:54 PM Aaron Marcuse-Kubitza

scripts/Makefile: Made read command syntax compatible with /bin/sh

237 12/21/2011 01:37 PM Aaron Marcuse-Kubitza

scripts/Makefile: Ignore errors about missing packages

236 12/21/2011 01:30 PM Aaron Marcuse-Kubitza

scripts/Makefile: Fixed escape character for /bin/sh

235 12/21/2011 01:25 PM Aaron Marcuse-Kubitza

scripts/Makefile: Added dependency installation. Makefiles: Use _not_file instead of FORCE for clarity. Use $(os) var

234 12/20/2011 07:52 PM Aaron Marcuse-Kubitza

fix_permissions: Configured output verbosity

233 12/20/2011 07:44 PM Aaron Marcuse-Kubitza

Added fix_permissions to set correct permissions on shared bien files

232 12/20/2011 07:31 PM Aaron Marcuse-Kubitza

Removed VegBank scripts which are no longer needed

231 12/20/2011 07:30 PM Aaron Marcuse-Kubitza

Removed VegBank scripts which are no longer needed

230 12/20/2011 06:55 PM Aaron Marcuse-Kubitza

Renamed vegbien_dest.sh to vegbien_dest to reflect that it is also includable by Makefiles

229 12/20/2011 06:52 PM Aaron Marcuse-Kubitza

DB user creation: Clarified instructions

228 12/20/2011 06:51 PM Aaron Marcuse-Kubitza

scripts/Makefile includes vegbien_dest.sh directly

227 12/20/2011 06:28 PM Aaron Marcuse-Kubitza

Moved db user creation to scripts/Makefile. Removed now-unneeded admin scripts.

226 12/20/2011 06:12 PM Aaron Marcuse-Kubitza

Removed VegBank scripts which are no longer needed

225 12/20/2011 06:11 PM Aaron Marcuse-Kubitza

scripts/Makefile: Added empty_db target which uses vegbien_empty.sql

224 12/20/2011 05:55 PM Aaron Marcuse-Kubitza

mappings/Makefile: Fixed bug where var containing prerequisistes needed to be defined before used. Added support for different sed flags to use extended regular expressions.

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