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# Date Author Comment
342 01/03/2012 01:13 PM Aaron Marcuse-Kubitza

exc.py: Added print_ex()

341 01/03/2012 01:13 PM Aaron Marcuse-Kubitza

util.py: Added type_name()

340 01/03/2012 01:12 PM Aaron Marcuse-Kubitza

strings.py: Added ensure_newl()

339 01/03/2012 11:42 AM Aaron Marcuse-Kubitza

input.Makefile: Save map output in log file

338 01/03/2012 11:27 AM Aaron Marcuse-Kubitza

bin/map: Print usage message when run with no arguments

337 01/03/2012 10:10 AM Aaron Marcuse-Kubitza

Makefile: Removed unnecessary commenting out of "allow from 127.0.0.0..." lines in /etc/phppgadmin/apache.conf

336 12/29/2011 05:35 PM Aaron Marcuse-Kubitza

Makefile: Use --loose-exit-status for ed to avoid failing on no match. In editPhppgadminApacheConf, use ,s/// instead of /.../\ns/// to match lines regardless of position.

335 12/29/2011 05:17 PM Aaron Marcuse-Kubitza

Makefile: Use tee instead of ed in sudoAppend. Don't change apache port to 8080 if apache already running on 80.

334 12/29/2011 04:54 PM Aaron Marcuse-Kubitza

Makefile: Added phppgadmin apache config

333 12/29/2011 01:16 PM Aaron Marcuse-Kubitza

bin/map: Only treat DatabaseErrors as warnings, not all Exceptions

332 12/29/2011 01:04 PM Aaron Marcuse-Kubitza

xml_func.py: Print newline before func XML because XML is now pretty-printed with indents

331 12/29/2011 12:59 PM Aaron Marcuse-Kubitza

xml_dom.py: Node.__str__() uses toprettyxml() instead of toxml()

330 12/29/2011 12:58 PM Aaron Marcuse-Kubitza

util.py: Changed rename_key() not to suppress KeyError, since some callers might want to assert that a key exists

329 12/29/2011 12:44 PM Aaron Marcuse-Kubitza

Makefile: Added phpPgAdmin dependency

328 12/29/2011 12:42 PM Aaron Marcuse-Kubitza

xml_func.py: _name func doesn't require all name parts to be set. _namePart func throws SyntaxException for invalid name parts.

327 12/28/2011 02:03 PM Aaron Marcuse-Kubitza

bin/map: Fixed syntax error where db variable had not been renamed to out_db

326 12/28/2011 01:58 PM Aaron Marcuse-Kubitza

xml_func.py: Generate SyntaxExceptions on missing XML func args

325 12/28/2011 01:46 PM Aaron Marcuse-Kubitza

VegX-VegBank mapping: Added default soilObs.soilHorizon value

324 12/28/2011 01:33 PM Aaron Marcuse-Kubitza

xml_func.py: Changed _date func to try parsing date field, rather than year field, as a decimal. Changed SALVIAS mappings to use new _date func syntax. Fixes SALVIAS plots data syntax error for decimal years.

323 12/28/2011 01:10 PM Aaron Marcuse-Kubitza

Removed no longer needed VegBank accepted test outputs

322 12/28/2011 01:09 PM Aaron Marcuse-Kubitza

test/map: Abort tester on failed diff

321 12/28/2011 01:09 PM Aaron Marcuse-Kubitza

Added accepted test output SALVIAS_db.organisms.VegBIEN.xml

320 12/28/2011 01:04 PM Aaron Marcuse-Kubitza

SALVIAS organisms mapping: Use _alt to merge tag1 and tag2. Fixes failing diff due to duplicate stemCodes.

319 12/28/2011 12:49 PM Aaron Marcuse-Kubitza

test/map: Added tests to insert VegBIEN XML into VegBIEN db

318 12/28/2011 12:47 PM Aaron Marcuse-Kubitza

bin/map: Fixed non-map input to set out_label

317 12/28/2011 12:12 PM Aaron Marcuse-Kubitza

bin/map: Fixed row processing when no map is used

316 12/28/2011 12:06 PM Aaron Marcuse-Kubitza

bin/map: Refactored to process each row separately when out_is_db

315 12/28/2011 12:04 PM Aaron Marcuse-Kubitza

xml_dom.py: Added Node pop() and clear() methods

314 12/28/2011 11:15 AM Aaron Marcuse-Kubitza

bin/map: Moved process_rows() exception handling around entire row, rather than each value, so that a broken value will not be ignored only to cause errors when outputing the row

313 12/28/2011 11:12 AM Aaron Marcuse-Kubitza

bin/map: Moved process_rows() exception handling around entire row, rather than each value, so that a broken value will not be ignored only to cause errors when outputing the row

312 12/28/2011 11:05 AM Aaron Marcuse-Kubitza

db_xml.py: Removed no longer needed xml2db()

311 12/28/2011 11:04 AM Aaron Marcuse-Kubitza

bin/map: out_is_db uses use_row instead of xml2db()

310 12/28/2011 10:53 AM Aaron Marcuse-Kubitza

bin/map: Added commit and exception-handling code to out_is_db use_row()

309 12/28/2011 10:42 AM Aaron Marcuse-Kubitza

bin/map: Merged get_xml() into process_xml(). Renamed process*() functions to distinguish them better.

308 12/28/2011 10:33 AM Aaron Marcuse-Kubitza

bin/map: Create separate document for printing XML opening and closing

307 12/28/2011 10:28 AM Aaron Marcuse-Kubitza

bin/map: Refactored to print document opening, contents, and closing in separate steps so they can be separated later

306 12/28/2011 10:27 AM Aaron Marcuse-Kubitza

xml_dom.py: Added support for integer indents

305 12/28/2011 10:19 AM Aaron Marcuse-Kubitza

xml_dom.py: Added NodeIter() and Node.__iter__()

304 12/28/2011 10:05 AM Aaron Marcuse-Kubitza

Use new xml_dom.prettyxml_config instead of Node.writeprettyxml because it can be passed as keyword args to any writexml function

303 12/28/2011 10:00 AM Aaron Marcuse-Kubitza

xml_dom.py: Removed no longer needed xml_dom.writexml()

302 12/28/2011 10:00 AM Aaron Marcuse-Kubitza

bin/map: Use Node.writeprettyxml() instead of xml_dom.writexml()

301 12/28/2011 09:57 AM Aaron Marcuse-Kubitza

xml_dom.py: Added minidom.Document write_opening() and write_closing() methods. Changed writexml(writer, node) to use new Node.writeprettyxml() method.

300 12/28/2011 09:28 AM Aaron Marcuse-Kubitza

Renamed ex.py to exc.py

299 12/28/2011 09:24 AM Aaron Marcuse-Kubitza

Import xml.dom.minidom as minidom

298 12/28/2011 09:10 AM Aaron Marcuse-Kubitza

xml_dom.py: Refactored xml.dom.minidom.Element.writexml() to use new write_opening() and write_closing() methods. Use new functions is_elem() and is_text_node() to determine node type. Corrected definition of a text element to be an element that contains a single text node.

297 12/28/2011 08:37 AM Aaron Marcuse-Kubitza

bin/map: Factored out input processing code

296 12/23/2011 04:03 PM Aaron Marcuse-Kubitza

Commit after inserting each row

295 12/23/2011 03:59 PM Aaron Marcuse-Kubitza

Commit after inserting each row

294 12/23/2011 03:54 PM Aaron Marcuse-Kubitza

Use traceback.print_exc() to print Exceptions for each row instead of exiting

293 12/23/2011 03:26 PM Aaron Marcuse-Kubitza

env_password: Allow user to change saved password

292 12/23/2011 03:14 PM Aaron Marcuse-Kubitza

env_password: Don't print instructions for storing password for the session if called to store password for the session

291 12/23/2011 03:00 PM Aaron Marcuse-Kubitza

env_password: Print absolute path to env_password in case invoking script changed the working directory

290 12/23/2011 02:57 PM Aaron Marcuse-Kubitza

env_password: Print instructions for storing password for the session

289 12/23/2011 02:32 PM Aaron Marcuse-Kubitza

Updated SALVIAS plots mappings and corresponding VegX-VegBank mappings to parse date_start and date_finish

288 12/23/2011 02:11 PM Aaron Marcuse-Kubitza

xml_func.py: Print XML of XML functions with SyntaxExceptions

287 12/23/2011 02:08 PM Aaron Marcuse-Kubitza

xml_func.py: Added support for parsing dates

286 12/23/2011 01:56 PM Aaron Marcuse-Kubitza

ex.py: repl_msg(): take replacements as keyword args

285 12/23/2011 01:44 PM Aaron Marcuse-Kubitza

fix_permissions: Also change user to bien

284 12/23/2011 01:31 PM Aaron Marcuse-Kubitza

Makefile: Added python-dateutil dependency

283 12/23/2011 12:57 PM Aaron Marcuse-Kubitza

input.Makefile: Renamed from_db-<map_file> target to import-<type> so it can be more easily run as a command-line target rather than just a prerequisite

282 12/23/2011 12:40 PM Aaron Marcuse-Kubitza

Added inputs/SALVIAS organisms map

281 12/22/2011 08:30 PM Aaron Marcuse-Kubitza

map: Print xml_func.SyntaxExceptions without stack traces by using SystemExit

280 12/22/2011 08:22 PM Aaron Marcuse-Kubitza

xml_func.py: Add function name to SyntaxException message

279 12/22/2011 08:22 PM Aaron Marcuse-Kubitza

ex.py: Added repl_msg() to format a message with the % operator

278 12/22/2011 07:48 PM Aaron Marcuse-Kubitza

xml_func.py: Return string->number conversion errors as xml_func.SyntaxExceptions

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