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From 12/07/2011 to 01/05/2012

01/05/2012

04:53 PM Task #311 (Resolved): Decouple VegBIEN from VegBank and map directly from VegX to VegBIEN
Decoupled VegBIEN from VegBank and removed mappings to VegBank Aaron Marcuse-Kubitza
03:07 PM Task #311 (Resolved): Decouple VegBIEN from VegBank and map directly from VegX to VegBIEN
Aaron Marcuse-Kubitza
04:48 PM Revision 382: Decoupled VegBIEN from VegBank and removed mappings to VegBank
Aaron Marcuse-Kubitza
04:30 PM Revision 381: Regenerate vegbien.sql by dumping the vegbien db
Aaron Marcuse-Kubitza
04:06 PM Revision 380: Regenerate vegbien.sql by dumping the vegbien db
Aaron Marcuse-Kubitza
04:05 PM Revision 379: psql_vegbien: Changed to use postgres_vegbien
Aaron Marcuse-Kubitza
04:03 PM Revision 378: Added postgres_vegbien to run PostgreSQL command on the vegbien db
Aaron Marcuse-Kubitza
03:26 PM Revision 377: SALVIAS verification: Added plot methods
Aaron Marcuse-Kubitza
03:09 PM Task #315 (New): Import TurboVeg data
Aaron Marcuse-Kubitza
03:09 PM Task #314 (Resolved): Import CTFS data
* coordinate with Shash
* CTFS has a lot of stems data
Aaron Marcuse-Kubitza
03:08 PM Task #313 (Resolved): Import full NYBG data
Aaron Marcuse-Kubitza
03:08 PM Task #312 (Resolved): Finish importing SALVIAS data
# -Import stems data-
# -Fix data format issues-: _Not sure what these were, probably long fixed_
# -Map invalid da...
Aaron Marcuse-Kubitza
01:19 PM Revision 376: SALVIAS verification: Added # plots
Aaron Marcuse-Kubitza
01:06 PM Revision 375: Makefile: Added targets to run input targets on all inputs
Aaron Marcuse-Kubitza
12:54 PM Revision 374: SALVIAS verification: Added projects list to examine why project counts differ
Aaron Marcuse-Kubitza
12:41 PM Revision 373: SALVIAS verification: Made statement-label SELECT statements use the same syntax for MySQL and PostgreSQL so they are easy to copy and paste between the input and output queries
Aaron Marcuse-Kubitza
11:26 AM Task #290: benchmark tests for database loading
You can view the validation results by running the following on vegbiendev:
@make verify --directory=/home/bien/svn/...
Aaron Marcuse-Kubitza
11:25 AM Task #305: Complete full-dataset validations for NYBG & SALVIAS
You can view the validation results by running the following on vegbiendev:
@make verify --directory=/home/bien/svn/...
Aaron Marcuse-Kubitza
11:25 AM Task #302: Make changes to VegBIEN schema
The vegbien db now contains some of the modifications Bob Peet made to the VegBank schema for VegBIEN, so some table ... Aaron Marcuse-Kubitza
11:24 AM Task #304: Complete full dataset imports to VegBIEN via VegX of NYBG and SALVIAS
I loaded the SALVIAS data (plots and organisms) into VegBIEN on vegbiendev. To browse the data, follow the [[phpPgAdm... Aaron Marcuse-Kubitza

01/04/2012

05:00 PM Task #305: Complete full-dataset validations for NYBG & SALVIAS
Created mechanism to write verification queries and compare to desired output Aaron Marcuse-Kubitza
04:57 PM Task #304: Complete full dataset imports to VegBIEN via VegX of NYBG and SALVIAS
Core SALVIAS data (plots and organisms) are on vegbiendev in VegBIEN.
Takes overnight to reinsert organisms data whe...
Aaron Marcuse-Kubitza
04:54 PM Revision 372: input.Makefile: Don't remove logs in clean
Aaron Marcuse-Kubitza
04:49 PM Task #303: Mapping from VegBIEN to original VegBank
Search-and-replace operations that transform VegBank to VegBIEN can in many cases be reversed to transform VegBIEN to... Aaron Marcuse-Kubitza
04:48 PM Task #302: Make changes to VegBIEN schema
All functions that used to output to VegBank now output to VegBIEN db.
The VegBIEN schema is automatically generated...
Aaron Marcuse-Kubitza
04:45 PM Task #296: Direct mapping from native salvias_plots MySQL database to VegBIEN
We will also need to import the projects, stems, and lookup_MethodCode tables in order for all the verification queri... Aaron Marcuse-Kubitza
04:43 PM Task #290: benchmark tests for database loading
Created mechanism to write verification queries and compare to desired output Aaron Marcuse-Kubitza
04:32 PM Revision 371: input.Makefile: Added support for multi-column verification queries. inputs/SALVIAS: Added a multi-column verification query.
Aaron Marcuse-Kubitza
03:47 PM Revision 370: input.Makefile: Remove all *.out in clean
Aaron Marcuse-Kubitza
02:59 PM Revision 369: inputs: Don't keep *.out under version control
Aaron Marcuse-Kubitza
02:35 PM Revision 368: input.Makefile: Added rules to verify inserted data and run tests
Aaron Marcuse-Kubitza
11:38 AM Revision 367: Regenerated inputs/SALVIAS/map.VegBIEN.1.organisms.csv
Aaron Marcuse-Kubitza
11:32 AM Revision 366: exc.py: Print ! before error messages so they can be found and counted more easily in log files
Aaron Marcuse-Kubitza
11:13 AM Revision 365: input.Makefile: Only output to log if importing all rows
Aaron Marcuse-Kubitza
10:46 AM Revision 364: Moved vegbien CREATE DATABASE command to Makefile and run vegbien.sql as bien user
Aaron Marcuse-Kubitza
10:27 AM Revision 363: Renamed vegbien tables according to Bob Peet's new VegBank-VegBIEN mapping
Aaron Marcuse-Kubitza
10:16 AM Revision 362: input.Makefile: Don't print commands that use set -x to be echoed
Aaron Marcuse-Kubitza
10:14 AM Revision 361: input.Makefile: Use system's time utility instead of shell's time command
Aaron Marcuse-Kubitza
10:09 AM Revision 360: sql.py: Include sql.DbException in DatabaseErrors list
Aaron Marcuse-Kubitza

01/03/2012

04:28 PM Revision 359: Generate VegX-VegBIEN.organisms.csv from VegBank-VegBIEN.map.csv, which is generated from VegBank-VegBIEN.map_only.csv
Aaron Marcuse-Kubitza
04:21 PM Revision 358: repl: Process whole file as one string so that regexps can match EOF for appending
Aaron Marcuse-Kubitza
04:21 PM Revision 357: mappings/Makefile: Clean *-VegBIEN.*.csv maps
Aaron Marcuse-Kubitza
04:08 PM Revision 356: Generate VegBank-VegBIEN.schema.csv from VegBank-VegBIEN.schema_only.csv and VegBank-VegBIEN.csv
Aaron Marcuse-Kubitza
04:06 PM Revision 355: Added cat_csv to concatenate two spreadsheets
Aaron Marcuse-Kubitza
03:34 PM Revision 354: Removed no longer needed inputs/SALVIAS/db.sh
Aaron Marcuse-Kubitza
03:24 PM Revision 353: Add sort order prefixes to inputs/SALVIAS maps
Aaron Marcuse-Kubitza
02:49 PM Revision 352: VegX-VegBank organisms mapping: Added collectionDate mapping
Aaron Marcuse-Kubitza
02:36 PM Revision 351: VegX-VegBank organisms mapping: Added collectionDate mapping
Aaron Marcuse-Kubitza
02:36 PM Revision 350: mappings/Makefile: Sort VegX-VegBank organisms mapping automatically when anything that depends on it is remade
Aaron Marcuse-Kubitza
02:34 PM Revision 349: Added in_place to run a stream command on a file
Aaron Marcuse-Kubitza
02:14 PM Revision 348: join_sort: Use /bin/sh instead of /bin/bash
Aaron Marcuse-Kubitza
01:44 PM Revision 347: NYBG-VegX mapping: Removed no longer needed global stem count value
Aaron Marcuse-Kubitza
01:42 PM Revision 346: Renamed test/accept_output to accept
Aaron Marcuse-Kubitza
01:40 PM Revision 345: VegX-VegBank.organisms.csv: Made stemCount default to 1
Aaron Marcuse-Kubitza
01:17 PM Revision 344: bin/map: Print DatabaseErrors without stack traces
Aaron Marcuse-Kubitza
01:13 PM Revision 343: exc.py: Added print_ex()
Aaron Marcuse-Kubitza
01:13 PM Revision 342: exc.py: Added print_ex()
Aaron Marcuse-Kubitza
01:13 PM Revision 341: util.py: Added type_name()
Aaron Marcuse-Kubitza
01:12 PM Revision 340: strings.py: Added ensure_newl()
Aaron Marcuse-Kubitza
11:42 AM Revision 339: input.Makefile: Save map output in log file
Aaron Marcuse-Kubitza
11:27 AM Revision 338: bin/map: Print usage message when run with no arguments
Aaron Marcuse-Kubitza
10:10 AM Revision 337: Makefile: Removed unnecessary commenting out of "allow from 127.0.0.0..." lines in /etc/phppgadmin/apache.conf
Aaron Marcuse-Kubitza

12/29/2011

05:35 PM Revision 336: 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.
Aaron Marcuse-Kubitza
05:17 PM Revision 335: Makefile: Use tee instead of ed in sudoAppend. Don't change apache port to 8080 if apache already running on 80.
Aaron Marcuse-Kubitza
04:54 PM Revision 334: Makefile: Added phppgadmin apache config
Aaron Marcuse-Kubitza
01:16 PM Revision 333: bin/map: Only treat DatabaseErrors as warnings, not all Exceptions
Aaron Marcuse-Kubitza
01:04 PM Revision 332: xml_func.py: Print newline before func XML because XML is now pretty-printed with indents
Aaron Marcuse-Kubitza
12:59 PM Revision 331: xml_dom.py: Node.__str__() uses toprettyxml() instead of toxml()
Aaron Marcuse-Kubitza
12:58 PM Revision 330: util.py: Changed rename_key() not to suppress KeyError, since some callers might want to assert that a key exists
Aaron Marcuse-Kubitza
12:44 PM Revision 329: Makefile: Added phpPgAdmin dependency
Aaron Marcuse-Kubitza
12:42 PM Revision 328: xml_func.py: _name func doesn't require all name parts to be set. _namePart func throws SyntaxException for invalid name parts.
Aaron Marcuse-Kubitza

12/28/2011

02:03 PM Revision 327: bin/map: Fixed syntax error where db variable had not been renamed to out_db
Aaron Marcuse-Kubitza
01:58 PM Revision 326: xml_func.py: Generate SyntaxExceptions on missing XML func args
Aaron Marcuse-Kubitza
01:46 PM Revision 325: VegX-VegBank mapping: Added default soilObs.soilHorizon value
Aaron Marcuse-Kubitza
01:33 PM Revision 324: 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.
Aaron Marcuse-Kubitza
01:10 PM Revision 323: Removed no longer needed VegBank accepted test outputs
Aaron Marcuse-Kubitza
01:09 PM Revision 322: test/map: Abort tester on failed diff
Aaron Marcuse-Kubitza
01:09 PM Revision 321: Added accepted test output SALVIAS_db.organisms.VegBIEN.xml
Aaron Marcuse-Kubitza
01:04 PM Revision 320: SALVIAS organisms mapping: Use _alt to merge tag1 and tag2. Fixes failing diff due to duplicate stemCodes.
Aaron Marcuse-Kubitza
12:49 PM Revision 319: test/map: Added tests to insert VegBIEN XML into VegBIEN db
Aaron Marcuse-Kubitza
12:47 PM Revision 318: bin/map: Fixed non-map input to set out_label
Aaron Marcuse-Kubitza
12:12 PM Revision 317: bin/map: Fixed row processing when no map is used
Aaron Marcuse-Kubitza
12:06 PM Revision 316: bin/map: Refactored to process each row separately when out_is_db
Aaron Marcuse-Kubitza
12:04 PM Revision 315: xml_dom.py: Added Node pop() and clear() methods
Aaron Marcuse-Kubitza
11:15 AM Revision 314: 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
Aaron Marcuse-Kubitza
11:12 AM Revision 313: 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
Aaron Marcuse-Kubitza
11:05 AM Revision 312: db_xml.py: Removed no longer needed xml2db()
Aaron Marcuse-Kubitza
11:04 AM Revision 311: bin/map: out_is_db uses use_row instead of xml2db()
Aaron Marcuse-Kubitza
10:53 AM Revision 310: bin/map: Added commit and exception-handling code to out_is_db use_row()
Aaron Marcuse-Kubitza
10:42 AM Revision 309: bin/map: Merged get_xml() into process_xml(). Renamed process*() functions to distinguish them better.
Aaron Marcuse-Kubitza
10:33 AM Revision 308: bin/map: Create separate document for printing XML opening and closing
Aaron Marcuse-Kubitza
10:28 AM Revision 307: bin/map: Refactored to print document opening, contents, and closing in separate steps so they can be separated later
Aaron Marcuse-Kubitza
10:27 AM Revision 306: xml_dom.py: Added support for integer indents
Aaron Marcuse-Kubitza
10:19 AM Revision 305: xml_dom.py: Added NodeIter() and Node.__iter__()
Aaron Marcuse-Kubitza
10:05 AM Revision 304: Use new xml_dom.prettyxml_config instead of Node.writeprettyxml because it can be passed as keyword args to any writexml function
Aaron Marcuse-Kubitza
10:00 AM Revision 303: xml_dom.py: Removed no longer needed xml_dom.writexml()
Aaron Marcuse-Kubitza
10:00 AM Revision 302: bin/map: Use Node.writeprettyxml() instead of xml_dom.writexml()
Aaron Marcuse-Kubitza
09:57 AM Revision 301: xml_dom.py: Added minidom.Document write_opening() and write_closing() methods. Changed writexml(writer, node) to use new Node.writeprettyxml() method.
Aaron Marcuse-Kubitza
09:28 AM Revision 300: Renamed ex.py to exc.py
Aaron Marcuse-Kubitza
09:24 AM Revision 299: Import xml.dom.minidom as minidom
Aaron Marcuse-Kubitza
09:10 AM Revision 298: 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.
Aaron Marcuse-Kubitza
08:37 AM Revision 297: bin/map: Factored out input processing code
Aaron Marcuse-Kubitza

12/23/2011

04:03 PM Revision 296: Commit after inserting each row
Aaron Marcuse-Kubitza
03:59 PM Revision 295: Commit after inserting each row
Aaron Marcuse-Kubitza
03:54 PM Revision 294: Use traceback.print_exc() to print Exceptions for each row instead of exiting
Aaron Marcuse-Kubitza
03:26 PM Revision 293: env_password: Allow user to change saved password
Aaron Marcuse-Kubitza
03:14 PM Revision 292: env_password: Don't print instructions for storing password for the session if called *to* store password for the session
Aaron Marcuse-Kubitza
03:00 PM Revision 291: env_password: Print absolute path to env_password in case invoking script changed the working directory
Aaron Marcuse-Kubitza
02:57 PM Revision 290: env_password: Print instructions for storing password for the session
Aaron Marcuse-Kubitza
02:32 PM Revision 289: Updated SALVIAS plots mappings and corresponding VegX-VegBank mappings to parse date_start and date_finish
Aaron Marcuse-Kubitza
02:11 PM Revision 288: xml_func.py: Print XML of XML functions with SyntaxExceptions
Aaron Marcuse-Kubitza
02:08 PM Revision 287: xml_func.py: Added support for parsing dates
Aaron Marcuse-Kubitza
01:56 PM Revision 286: ex.py: repl_msg(): take replacements as keyword args
Aaron Marcuse-Kubitza
01:44 PM Revision 285: fix_permissions: Also change user to bien
Aaron Marcuse-Kubitza
01:31 PM Revision 284: Makefile: Added python-dateutil dependency
Aaron Marcuse-Kubitza
12:57 PM Revision 283: 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
Aaron Marcuse-Kubitza
12:40 PM Revision 282: Added inputs/SALVIAS organisms map
Aaron Marcuse-Kubitza

12/22/2011

08:30 PM Revision 281: map: Print xml_func.SyntaxExceptions without stack traces by using SystemExit
Aaron Marcuse-Kubitza
08:22 PM Revision 280: xml_func.py: Add function name to SyntaxException message
Aaron Marcuse-Kubitza
08:22 PM Revision 279: ex.py: Added repl_msg() to format a message with the % operator
Aaron Marcuse-Kubitza
07:48 PM Revision 278: xml_func.py: Return string->number conversion errors as xml_func.SyntaxExceptions
Aaron Marcuse-Kubitza
07:29 PM Revision 277: psql_vegbien: Fixed comment to vegbien instead of vegbank
Aaron Marcuse-Kubitza
07:11 PM Revision 276: psql_vegbien: Use new location of bien_password
Aaron Marcuse-Kubitza
07:05 PM Revision 275: Makefile: Fixed paths to mappings dir for new scripts dir location
Aaron Marcuse-Kubitza
07:02 PM Revision 274: Renamed util to bin
Aaron Marcuse-Kubitza
06:59 PM Revision 273: Moved inputs_Makefile to inputs/input.Makefile
Aaron Marcuse-Kubitza
06:55 PM Revision 272: Moved bien_password to new config dir
Aaron Marcuse-Kubitza
06:52 PM Revision 271: Moved sample inputs to test dir
Aaron Marcuse-Kubitza
06:42 PM Revision 270: Added symlink from scripts to new scripts destination
Aaron Marcuse-Kubitza
06:40 PM Revision 269: Removed now-empty scripts dir
Aaron Marcuse-Kubitza
06:39 PM Revision 268: Moved everything in scripts to root. inputs_Makefile: Don't run "all" when installing.
Aaron Marcuse-Kubitza
06:24 PM Revision 267: Renamed bien_map to map
Aaron Marcuse-Kubitza
06:22 PM Revision 266: Moved map to util
Aaron Marcuse-Kubitza
06:14 PM Revision 265: fix_permissions: Don't chmod symlinks
Aaron Marcuse-Kubitza
06:00 PM Revision 264: inputs_Makefile: Auto-generate map to VegBIEN and import data into vegbien from input DB
Aaron Marcuse-Kubitza
05:59 PM Revision 263: inputs/SALVIAS: maps to VegX and VegBIEN
Aaron Marcuse-Kubitza
05:58 PM Revision 262: bien_map: Runs map with BIEN defaults
Aaron Marcuse-Kubitza
05:56 PM Revision 261: join_sort: Sorts a join on the output col
Aaron Marcuse-Kubitza
03:20 PM Revision 260: inputs_Makefile: Require dbEngine var instead of defaulting to MySQL
Aaron Marcuse-Kubitza
02:22 PM Revision 259: Moved inputs into svn
Aaron Marcuse-Kubitza
01:46 PM Revision 258: Moved pre-BIEN 3 files into _archive folder
Aaron Marcuse-Kubitza
01:46 PM Revision 257: test/map: Use db.sh syntax in *.sh tests
Aaron Marcuse-Kubitza
01:45 PM Revision 256: inputs_Makefile: Generate db.sh with DB access info
Aaron Marcuse-Kubitza
12:59 PM Revision 255: 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.
Aaron Marcuse-Kubitza
12:41 PM Task #302: Make changes to VegBIEN schema
Bob Peet's changes are at [[VegBIEN from VegBank]]
E-mail from Bob Peet on 2011-12-22:
I promised to summarize ...
Aaron Marcuse-Kubitza
12:31 PM Task #310 (Resolved): automated build process
I set up an automated build process for all the BIEN scripts and dependencies. It runs on both vegbiendev and nimoy. ... Aaron Marcuse-Kubitza
12:31 PM Task #310 (Resolved): automated build process
Aaron Marcuse-Kubitza
12:30 PM Revision 254: scripts/Makefile: Added action for postgres-Darwin target
Aaron Marcuse-Kubitza
12:11 PM Revision 253: scripts/Makefile: Added postgresql to postgres-Linux apt-get packages
Aaron Marcuse-Kubitza

12/21/2011

08:23 PM Revision 252: test/map: Changed to work on both nimoy and vegbiendev by selecting the appropriate MySQL user and password
Aaron Marcuse-Kubitza
08:22 PM Revision 251: env_password: Added optional message arg
Aaron Marcuse-Kubitza
07:47 PM Revision 250: Added uninstallation of inputs to Makefiles
Aaron Marcuse-Kubitza
07:15 PM Revision 249: scripts/Makefile: Create bien user w/o prompting for password. Fixed syntax error.
Aaron Marcuse-Kubitza
07:06 PM Revision 248: scripts/Makefile: Fixed syntax error
Aaron Marcuse-Kubitza
07:03 PM Revision 247: Inputs now include inputs_Makefile to get mysql command, etc.
Aaron Marcuse-Kubitza
06:30 PM Revision 246: scripts/Makefile: Use bien MySQL user for installing inputs
Aaron Marcuse-Kubitza
06:26 PM Revision 245: scripts/Makefile: Use root MySQL user for creating bien user
Aaron Marcuse-Kubitza
05:53 PM Revision 244: scripts/Makefile: Don't use root as MySQL admin user. Removed no-longer-needed sub-makes for setting DB login vars.
Aaron Marcuse-Kubitza
05:10 PM Revision 243: Changed vegbien_dest and users of it to use separate bien_password file
Aaron Marcuse-Kubitza
04:55 PM Revision 242: fix_permissions: Extend all user permissions to group
Aaron Marcuse-Kubitza
04:26 PM Revision 241: scripts/Makefile: Added inputs
Aaron Marcuse-Kubitza
03:24 PM Revision 240: mappings/Makefile: Cleaned up
Aaron Marcuse-Kubitza
03:02 PM Revision 239: fix_permissions: Don't add group write perms to read-only files
Aaron Marcuse-Kubitza
01:54 PM Revision 238: scripts/Makefile: Made read command syntax compatible with /bin/sh
Aaron Marcuse-Kubitza
01:37 PM Revision 237: scripts/Makefile: Ignore errors about missing packages
Aaron Marcuse-Kubitza
01:30 PM Revision 236: scripts/Makefile: Fixed escape character for /bin/sh
Aaron Marcuse-Kubitza
01:25 PM Revision 235: scripts/Makefile: Added dependency installation. Makefiles: Use _not_file instead of FORCE for clarity. Use $(os) var
Aaron Marcuse-Kubitza

12/20/2011

07:52 PM Revision 234: fix_permissions: Configured output verbosity
Aaron Marcuse-Kubitza
07:44 PM Revision 233: Added fix_permissions to set correct permissions on shared bien files
Aaron Marcuse-Kubitza
07:31 PM Revision 232: Removed VegBank scripts which are no longer needed
Aaron Marcuse-Kubitza
07:30 PM Revision 231: Removed VegBank scripts which are no longer needed
Aaron Marcuse-Kubitza
06:55 PM Revision 230: Renamed vegbien_dest.sh to vegbien_dest to reflect that it is also includable by Makefiles
Aaron Marcuse-Kubitza
06:52 PM Revision 229: DB user creation: Clarified instructions
Aaron Marcuse-Kubitza
06:51 PM Revision 228: scripts/Makefile includes vegbien_dest.sh directly
Aaron Marcuse-Kubitza
06:28 PM Revision 227: Moved db user creation to scripts/Makefile. Removed now-unneeded admin scripts.
Aaron Marcuse-Kubitza
06:12 PM Revision 226: Removed VegBank scripts which are no longer needed
Aaron Marcuse-Kubitza
06:11 PM Revision 225: scripts/Makefile: Added empty_db target which uses vegbien_empty.sql
Aaron Marcuse-Kubitza
05:55 PM Revision 224: 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.
Aaron Marcuse-Kubitza
05:42 PM Revision 223: Added auto-generated vegbien_empty.sql to empty the vegbien db
Aaron Marcuse-Kubitza
04:55 PM Revision 222: Test output to VegBIEN instead of VegBank
Aaron Marcuse-Kubitza
04:54 PM Revision 221: VegX-VegBIEN.organisms.csv: sort output of repl
Aaron Marcuse-Kubitza
04:46 PM Revision 220: review: Added nullglob
Aaron Marcuse-Kubitza
04:44 PM Revision 219: review: Don't process replacements spreadsheets
Aaron Marcuse-Kubitza
04:44 PM Revision 218: Moved schema replacements from VegBank-VegBIEN.csv to VegBank-VegBIEN.schema.csv
Aaron Marcuse-Kubitza
04:32 PM Revision 217: VegBank-VegBIEN.csv: Support PostgreSQL before 8.4
Aaron Marcuse-Kubitza
04:29 PM Revision 216: repl: Added support for blank lines. Only add whole word regexp code to inputs w/o *any* regexp metachars.
Aaron Marcuse-Kubitza
04:13 PM Revision 215: Create vegbien db from mappings/schemas/vegbien.sql
Aaron Marcuse-Kubitza
04:12 PM Revision 214: VegBank-VegBIEN.csv: Added replacements for SQL create script conversion
Aaron Marcuse-Kubitza
03:56 PM Revision 213: Generate vegbien db create SQL from vegbank.sql using repl
Aaron Marcuse-Kubitza
03:55 PM Revision 212: Generate vegbien db create SQL from vegbank.sql using repl
Aaron Marcuse-Kubitza
03:54 PM Revision 211: repl: Fixed bug in reading arguments
Aaron Marcuse-Kubitza
03:38 PM Revision 210: repl: Don't add whole-word regexp for inputs that already have regexp metachars
Aaron Marcuse-Kubitza
03:26 PM Revision 209: Removed mappings/VegBank-VegBIEN.organisms.csv because now using replacements spreadsheet
Aaron Marcuse-Kubitza
03:24 PM Revision 208: mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet
Aaron Marcuse-Kubitza
03:23 PM Revision 207: mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet
Aaron Marcuse-Kubitza
03:23 PM Revision 206: mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet
Aaron Marcuse-Kubitza
02:57 PM Revision 205: Added repl to perform replacements on a spreadsheet or file
Aaron Marcuse-Kubitza
01:38 PM Revision 204: scripts/Makefile: removed extra test-% target
Aaron Marcuse-Kubitza
01:38 PM Revision 203: README.TXT: Updated
Aaron Marcuse-Kubitza
01:36 PM Revision 202: scripts/Makefile: install/uninstall targets
Aaron Marcuse-Kubitza
01:36 PM Revision 201: bien_user_create: Print instructions in sequence with password prompts
Aaron Marcuse-Kubitza

12/19/2011

06:16 PM Revision 200: mappings to VegBIEN: Accounted for remaining ALTER TABLE statements
Aaron Marcuse-Kubitza
05:48 PM Revision 199: Renamed format*_for_review to review and added for_review to make clean
Aaron Marcuse-Kubitza
05:41 PM Revision 198: mappings: Added mappings to VegBIEN
Aaron Marcuse-Kubitza
05:25 PM Revision 197: mappings/Makefile: Simplified
Aaron Marcuse-Kubitza
05:22 PM Revision 196: mappings/Makefile: Simplified
Aaron Marcuse-Kubitza
04:59 PM Revision 195: README.TXT: Updated
Aaron Marcuse-Kubitza
04:47 PM Revision 194: Added vegbien DB admin scripts
Aaron Marcuse-Kubitza

12/16/2011

03:54 PM Revision 193: join_all_vegbank: Sort output by both columns
Aaron Marcuse-Kubitza
03:48 PM Revision 192: mappings/VegX-VegBank.organisms.csv: Sorted by both columns
Aaron Marcuse-Kubitza
03:48 PM Revision 191: mappings/Makefile: Sort VegBank-VegBIEN.organisms.csv by both columns
Aaron Marcuse-Kubitza
03:47 PM Revision 190: extract_plot_map: Removed because functionality now in Makefile
Aaron Marcuse-Kubitza
03:46 PM Revision 189: sort: Can sort on multiple columns
Aaron Marcuse-Kubitza
03:17 PM Revision 188: Added basic VegX-VegBIEN mapping
Aaron Marcuse-Kubitza
02:02 PM Revision 187: Added union and join_passthru
Aaron Marcuse-Kubitza
02:02 PM Revision 186: env_password: Print Usage message to stderr
Aaron Marcuse-Kubitza
01:29 PM Revision 185: test/map: Create output dir if it doesn't exist
Aaron Marcuse-Kubitza
01:24 PM Revision 184: Converted scripts back to bash that required bash-specific features
Aaron Marcuse-Kubitza
01:23 PM Revision 183: Converted scripts back to bash that required bash-specific features
Aaron Marcuse-Kubitza
01:13 PM Revision 182: Fixed test/map to work with sh
Aaron Marcuse-Kubitza
01:05 PM Revision 181: Replaced /bin/bash with /bin/sh
Aaron Marcuse-Kubitza
12:31 PM Task #300: TurboVeg data
Mike Lee's mapping is on nimoy under @/home/bien_shared/raw_data/turboveg/DBASEDIC_rkp2011_mtl2011.xlsx@ Aaron Marcuse-Kubitza
12:21 PM Task #309 (Rejected): mapping and export utility from VegBank to VegX
Ideally, what I have in mind is mapping and export utility from VegBank to VegX. Of course this means more work up fr... Aaron Marcuse-Kubitza
12:20 PM Task #308 (Resolved): do a direct transfer of some public data from VegBank
Even higher priority, do you think you could set us up to do a direct transfer of some public data from VegBank? At t... Aaron Marcuse-Kubitza

12/15/2011

04:16 PM Revision 180: join: Added usage item for repeated joins
Aaron Marcuse-Kubitza
04:13 PM Revision 179: join: Changed order of args and redirects to be more intuitive
Aaron Marcuse-Kubitza
04:09 PM Revision 178: Renamed ch_map_root to ch_root
Aaron Marcuse-Kubitza
04:08 PM Revision 177: Renamed join_maps to join
Aaron Marcuse-Kubitza
03:42 PM Task #307 (Resolved): Acquire additional specimen data sets in both DwC and DwCA format, esp. GBIF
Aaron Marcuse-Kubitza
03:42 PM Task #306 (Resolved): Acquire additional plot data sets from providers willing to work with Aaron on mappings and validations
Bob: TurboVeg; Brad: RAINFOR, CTFS Aaron Marcuse-Kubitza
03:42 PM Task #305 (Resolved): Complete full-dataset validations for NYBG & SALVIAS
Aaron Marcuse-Kubitza
03:41 PM Task #304 (Resolved): Complete full dataset imports to VegBIEN via VegX of NYBG and SALVIAS
* Identify and make changes to VegX needed to enable full-dataset imports
* Or report changes needed to Nick, Miquel...
Aaron Marcuse-Kubitza
03:41 PM Task #303 (New): Mapping from VegBIEN to original VegBank
the latter to be used as web schema for BIEN web interface Aaron Marcuse-Kubitza
03:40 PM Task #302 (Resolved): Make changes to VegBIEN schema
Aaron Marcuse-Kubitza
02:49 PM Task #294: find plot data source provider to work with Aaron
Brad has contacted two data source provider (RAINFOR, CTFS) regarding working with Aaron to develop mappings Brad Boyle
01:55 PM Task #285 (Resolved): CSV to XML mappings for NYBG, SALVIAS
initial data sources NYBG and SALVIAS have been fully mapped Aaron Marcuse-Kubitza
01:53 PM Task #291 (Resolved): list of milestones
got commented milestones from Martha Aaron Marcuse-Kubitza
01:03 PM Task #286: CSV-XML-database mapping script
I added support for mapping XML to XML, which will enable us to process NVS's VegX data, and eventually also their in... Aaron Marcuse-Kubitza
01:03 PM Task #296: Direct mapping from native salvias_plots MySQL database to VegBIEN
I added a new mapping to get SALVIAS data directly from the salvias_plots database on nimoy. You can see the results ... Aaron Marcuse-Kubitza
12:20 PM Revision 176: Merged test Makefile into main scripts Makefile
Aaron Marcuse-Kubitza
12:05 PM Revision 175: test/map: Turn off test mode (don't run diff) when env var n (for # rows) is set
Aaron Marcuse-Kubitza
11:39 AM Revision 174: Added SALVIAS DB mapping for plots data
Aaron Marcuse-Kubitza
11:37 AM Revision 173: VegX-VegBank mapping: Fixed VegBank XPath for commName.commName field
Aaron Marcuse-Kubitza
11:35 AM Revision 172: 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.
Aaron Marcuse-Kubitza
11:31 AM Revision 171: 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.
Aaron Marcuse-Kubitza

12/14/2011

05:31 PM Revision 170: xpath.py: Moved abbr expansion code to separate function
Aaron Marcuse-Kubitza
04:41 PM Revision 169: test/map: Process all tables for a given DB (.sh) input
Aaron Marcuse-Kubitza
03:26 PM Revision 168: Removed /'s from DB input mappings
Aaron Marcuse-Kubitza
02:29 PM Task #299: Mapping from NVS to VegX and VegBIEN
NVS data from Nick Spencer is on nimoy in @/home/bien_shared/raw_data/nvs/@ Aaron Marcuse-Kubitza
02:06 PM Task #299 (Resolved): Mapping from NVS to VegX and VegBIEN
Will require finding someone at NVS willing to work with Aaron and mappings and validations Aaron Marcuse-Kubitza
02:25 PM Task #300: TurboVeg data
TurboVeg info from Bob Peet is on nimoy in @/home/bien_shared/raw_data/turboveg/@ Aaron Marcuse-Kubitza
02:07 PM Task #300 (New): TurboVeg data
with commitment by someone familiar with DB to work with Aaron on (a) evaluating mappings, and (b) developing validat... Aaron Marcuse-Kubitza
02:07 PM Task #301 (Resolved): RAINFOR data
with commitment by someone familiar with DB to work with Aaron on (a) evaluating mappings, and (b) developing validat... Aaron Marcuse-Kubitza
02:06 PM Task #298 (New): Try to find source of DwCA (DwC Archives) data
hoping GBIF will be willing to work with us on this. Possibly approach Remsen directly Aaron Marcuse-Kubitza
02:05 PM Task #297 (Resolved): Request new data dump of specimen data from GBIF, this time in DwC format
Aaron Marcuse-Kubitza
02:03 PM Task #296 (Resolved): Direct mapping from native salvias_plots MySQL database to VegBIEN
Aaron Marcuse-Kubitza
01:59 PM Task #289: look for formal mapping mechanism
Got NVS mapping tool from Nick Spencer, which is on nimoy in @/home/bien_shared/raw_data/nvs/VegX/@ Aaron Marcuse-Kubitza
01:54 PM Task #286: CSV-XML-database mapping script
Added support for database and XML inputs Aaron Marcuse-Kubitza
01:46 PM Revision 167: map: Use row's index instead of pkey as ID in XML output
Aaron Marcuse-Kubitza
01:45 PM Revision 166: test/map: Compare via-VegX output to direct output
Aaron Marcuse-Kubitza
01:13 PM Revision 165: 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
Aaron Marcuse-Kubitza
12:03 PM Revision 164: map: Handle metadata in order with regular mappings
Aaron Marcuse-Kubitza
11:33 AM Revision 163: Accepted VegBank test output for new CSV mapping order
Aaron Marcuse-Kubitza
11:26 AM Revision 162: map: Changed CSV input to process mappings in the order they are in the spreadsheet, rather than the order of the CSV columns
Aaron Marcuse-Kubitza

12/13/2011

05:18 PM Revision 161: map: Added support for XML input
Aaron Marcuse-Kubitza
05:17 PM Revision 160: Accepted new test output for sorted SALVIAS_db-VegBank mapping
Aaron Marcuse-Kubitza
05:07 PM Revision 159: mappings to VegBank: Sorted by output column to help VegX-VegBank conversion put elements in the same order as source-VegBank
Aaron Marcuse-Kubitza
04:57 PM Revision 158: join_all_vegbank: Updated to sort output maps
Aaron Marcuse-Kubitza
04:57 PM Revision 157: Added script to sort a spreadsheet
Aaron Marcuse-Kubitza
03:51 PM Revision 156: xpath.py: Allowed empty names in XPaths
Aaron Marcuse-Kubitza
03:48 PM Revision 155: xpath.py: Added automatic conversion of strings to paths where needed.
Aaron Marcuse-Kubitza
03:00 PM Revision 154: xpath.py: Added caching of parsed XPaths. Added automatic conversion of strings to paths where needed.
Aaron Marcuse-Kubitza
02:59 PM Revision 153: Added __str__() method to XML nodes
Aaron Marcuse-Kubitza
02:58 PM Revision 152: Fixed VegX-VegBank mapping syntax error
Aaron Marcuse-Kubitza
02:17 PM Revision 151: Added faded beginning of string in Parser syntax errors
Aaron Marcuse-Kubitza
02:01 PM Revision 150: Updated mappings Makefile
Aaron Marcuse-Kubitza
02:00 PM Revision 149: Added Makefiles for scripts and test
Aaron Marcuse-Kubitza
01:54 PM Revision 148: Added mappings Makefile
Aaron Marcuse-Kubitza
12:28 PM Revision 147: Added human-readable SALVIAS_db mappings
Aaron Marcuse-Kubitza
12:28 PM Revision 146: db_xml.get(): Pass limit through to SQL query
Aaron Marcuse-Kubitza
12:11 PM Task #295 (Resolved): provide benchmark queries for NYBG data
Brad Boyle provided NYBG queries, which are on the wiki under [[NYBG tests]] Aaron Marcuse-Kubitza
12:10 PM Task #290: benchmark tests for database loading
Brad Boyle provided NYBG queries, which are on the wiki under [[NYBG tests]] Aaron Marcuse-Kubitza
11:57 AM Task #291: list of milestones
updated to do list Aaron Marcuse-Kubitza
11:56 AM Task #291: list of milestones
Brad created a timeline, which is on the wiki under [[December 8 2011 WebEx meeting]]. Aaron Marcuse-Kubitza
11:48 AM Revision 145: Regenerated human-readable mappings
Aaron Marcuse-Kubitza

12/12/2011

05:39 PM Revision 144: Fixed documentation for xml_funcs
Aaron Marcuse-Kubitza
05:38 PM Revision 143: Refactored xml_dom.set_value() to avoid needing a doc parameter for the XML document
Aaron Marcuse-Kubitza
05:35 PM Revision 142: xpath.py: Refactored xml_func.py to avoid needing a doc parameter for the XML document
Aaron Marcuse-Kubitza
05:30 PM Revision 141: xpath.py: Refactored to avoid needing a doc parameter for the XML document
Aaron Marcuse-Kubitza
04:41 PM Revision 140: Fixed DB input to ignore NULL values
Aaron Marcuse-Kubitza
04:27 PM Revision 139: xml_dom.py: Changed all uses of name_of(node) to node.tagName
Aaron Marcuse-Kubitza
04:23 PM Revision 138: Made XML node names case-sensitive
Aaron Marcuse-Kubitza
04:20 PM Revision 137: mappings to VegBank: Fixed incorrect mappings found after disabling heuristic search for missing fields
Aaron Marcuse-Kubitza
03:49 PM Revision 136: test/map: Ignore diff exit status
Aaron Marcuse-Kubitza
03:34 PM Revision 135: map: Implemented DB input support for querying a single table
Aaron Marcuse-Kubitza

12/09/2011

05:36 PM Revision 134: Added SALVIAS_db test accepted output
Aaron Marcuse-Kubitza
05:35 PM Revision 133: map: Continued to add DB input support
Aaron Marcuse-Kubitza
04:54 PM Revision 132: test/map: Echo command used to import db config
Aaron Marcuse-Kubitza
04:02 PM Revision 131: Added support for multiple database engines. Changed SALVIAS_db input to use user-entered password.
Aaron Marcuse-Kubitza
01:58 PM Revision 130: map: Allow db config vars to be optional. SALVIAS_db test: Changed to use salvias_plots and XPath mapping syntax.
Aaron Marcuse-Kubitza
01:32 PM Revision 129: Renamed SALVIAS_db test input to use organisms table
Aaron Marcuse-Kubitza
01:29 PM Revision 128: Re-committed accepted_outputs
Aaron Marcuse-Kubitza
01:23 PM Revision 127: Renamed test/map output to remove CSV/DB indicator because that is now specified in the datasource name
Aaron Marcuse-Kubitza
01:18 PM Revision 126: map: Started adding database get by XPath functionality
Aaron Marcuse-Kubitza

12/08/2011

06:48 PM Revision 125: format_for_review: Fixed bug where Comments column would be reformatted in addition to mappings columns
Aaron Marcuse-Kubitza
05:38 PM Task #285: CSV to XML mappings for NYBG, SALVIAS
To make it easier to review the mappings, I created human-readable versions "in Subversion":https://projects.nceas.uc... Aaron Marcuse-Kubitza
05:35 PM Revision 124: Regenerated human-readable mappings
Aaron Marcuse-Kubitza
05:15 PM Revision 123: Added human-readable versions of mappings and scripts to generate them
Aaron Marcuse-Kubitza
05:14 PM Revision 122: VegX-VegBank mapping: Removed a duplicated mapping
Aaron Marcuse-Kubitza
05:13 PM Revision 121: NYBG-VegX mapping: Added conference call feedback
Aaron Marcuse-Kubitza
03:12 PM Task #295 (Resolved): provide benchmark queries for NYBG data
Aaron Marcuse-Kubitza
03:11 PM Task #294 (Resolved): find plot data source provider to work with Aaron
Aaron Marcuse-Kubitza
01:48 PM Revision 120: Added Comments column with Brad's and Aaron's comments to mapping spreadsheets
Aaron Marcuse-Kubitza
01:07 PM Task #290: benchmark tests for database loading
Brad Boyle provided SALVIAS queries, which are on the wiki under [[SALVIAS tests]] Aaron Marcuse-Kubitza

12/07/2011

05:01 PM Revision 119: Added stub for SALVIAS database test
Aaron Marcuse-Kubitza
05:00 PM Revision 118: test/map: Added support for database input
Aaron Marcuse-Kubitza
04:14 PM Revision 117: Preparing map to input from DB
Aaron Marcuse-Kubitza
04:05 PM Task #288: VegX-VegBank mapping
If you would like to browse the @vegbank@ database on nimoy, you can now use "phpPgAdmin":http://bien.nceas.ucsb.edu/... Aaron Marcuse-Kubitza
03:47 PM Task #293: mapping inversion script
updated transformations Aaron Marcuse-Kubitza
01:43 PM Task #293: mapping inversion script
suggested name and location: @svn/scripts/util/invert_map@ Aaron Marcuse-Kubitza
01:41 PM Task #293 (New): mapping inversion script
A Python script to invert a mapping spreadsheet. This will be useful for mapping VegBank to VegX, so that we can just... Aaron Marcuse-Kubitza
03:32 PM Revision 116: Started preparing map to input from DB
Aaron Marcuse-Kubitza
02:18 PM Task #289: look for formal mapping mechanism
*"RDF SPARQL":http://en.wikipedia.org/wiki/SPARQL:*
* SELECT-style queries for RDF data
* uses concise Turtle syn...
Aaron Marcuse-Kubitza
02:01 PM Task #289: look for formal mapping mechanism
*"IBM Clio":http://www.almaden.ibm.com/cs/projects/criollo/:*
* "Clio then also interprets these mappings to const...
Aaron Marcuse-Kubitza
01:23 PM Task #289: look for formal mapping mechanism
updated to do list Aaron Marcuse-Kubitza
01:11 PM Task #289: look for formal mapping mechanism
*"Bourret's XML-ER mapping":http://rpbourret.com/:*
* *summary: his various mapping methods are already used by Ve...
Aaron Marcuse-Kubitza
12:45 PM Task #289: look for formal mapping mechanism
*XQuery:*
* "XQuery Tutorial":http://www.w3schools.com/xquery/default.asp
** XQuery iterates over XML documents stor...
Aaron Marcuse-Kubitza
12:38 PM Task #289: look for formal mapping mechanism
*Altova XMLSpy's graphical generation of XPaths:*
* *summary: XMLSpy and Oxygen XML both have Copy XPath commands (O...
Aaron Marcuse-Kubitza
01:27 PM Revision 115: xml_func.py: Added optimization to first check if function name starts with _ before looking it up in the table
Aaron Marcuse-Kubitza
12:24 PM Revision 114: Added _alt functions for mappings to VegBank authorPlotCode
Aaron Marcuse-Kubitza
12:17 PM Revision 113: xml_func.py: Added _alt function to choose between alternative values and used it for the collector plantName mapping
Aaron Marcuse-Kubitza
11:54 AM Revision 112: VegX-VegBank mapping: Added mapping from taxonName/Simple (NYBG ScientificName) to collector plantName so that collector plantName will always have a value
Aaron Marcuse-Kubitza
11:27 AM Revision 111: xml_func.py: Added support for decimal years (with day as the fraction)
Aaron Marcuse-Kubitza
11:16 AM Revision 110: test/map: Added echoing of commands run
Aaron Marcuse-Kubitza
 

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