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Name Size Revision Age Author Comment
  _archive 1598 almost 13 years Aaron Marcuse-Kubitza Moved _archive/tapir2flatClient/trunk/client/ t...
  analysis 3076 over 12 years Aaron Marcuse-Kubitza Added top-level analysis dir for range modeling
  backups 10267 over 11 years Aaron Marcuse-Kubitza backups/Makefile: %.backup/restore: documented ...
  bin 10447 over 11 years Aaron Marcuse-Kubitza bin/my2pg: commenting out table options: added ...
  config 7801 almost 12 years Aaron Marcuse-Kubitza root Makefile: VegBIEN DB: mk_db: Added command...
  exports 9928 over 11 years Aaron Marcuse-Kubitza added exports/_archive/
  inputs 10444 over 11 years Aaron Marcuse-Kubitza bin/my2pg: comment out COMMENTs instead of remo...
  lib 10446 over 11 years Aaron Marcuse-Kubitza lib/sh/db.sh: mysqldump(): don't use --compatib...
  mappings 10420 over 11 years Aaron Marcuse-Kubitza mappings/VegCore.htm: regenerated from wiki. ad...
  planning 10429 over 11 years Aaron Marcuse-Kubitza planning/timeline/timeline.2013.xls: Adding der...
  schemas 10446 over 11 years Aaron Marcuse-Kubitza lib/sh/db.sh: mysqldump(): don't use --compatib...
  web 10306 over 11 years Aaron Marcuse-Kubitza web/links/index.htm: updated to Firefox bookmar...
.htaccess 326 Bytes 8771 over 11 years Aaron Marcuse-Kubitza /.htaccess: use canonical URL without symlinks
.rsync_filter.upload 33 Bytes 10042 over 11 years Aaron Marcuse-Kubitza /.rsync_ignore: temp files: hide them on upload...
.rsync_ignore 12 Bytes 10042 over 11 years Aaron Marcuse-Kubitza /.rsync_ignore: temp files: hide them on upload...
Makefile 12.6 KB 10223 over 11 years Aaron Marcuse-Kubitza /Makefile: mysql-Linux: also install mysql-work...
README.TXT 23.3 KB 10379 over 11 years Aaron Marcuse-Kubitza /README.TXT: Maintenance: added instructions fo...
fix_perms 97 Bytes 7560 almost 12 years Aaron Marcuse-Kubitza Added root fix_perms
map 1001 Bytes 6949 about 12 years Aaron Marcuse-Kubitza vegbien_dest: Changed default $prefix to "", so...
new_terms.csv 38.1 KB 7222 almost 12 years Aaron Marcuse-Kubitza new_terms.csv: Regenerated
run 433 Bytes 9916 over 11 years Aaron Marcuse-Kubitza /run: geoscrub_input/make(): documented runtime...
unmapped_terms.csv 13.1 KB 7201 almost 12 years Aaron Marcuse-Kubitza **/new_terms.csv, **/unmapped_terms.csv: Regene...

Latest revisions

# Date Author Comment
10447 07/26/2013 08:09 PM Aaron Marcuse-Kubitza

bin/my2pg: commenting out table options: added explanatory comment, because it is not obvious from the regexp what this does

10446 07/26/2013 08:06 PM Aaron Marcuse-Kubitza

lib/sh/db.sh: mysqldump(): don't use --compatible=postgresql when the table structure is being exported, because this removes the table options (which include the COMMENT attribute). --compatible=postgresql remains on in data-only mode because embedded ` in data cannot easily be distinguished from ` around column names, so ANSI_QUOTES is needed to do the translation to " (and data sections do not contain table options). note that all --compatible modes that offer ANSI_QUOTES unfortunately exclude the table options, and there is no way to run a SQL query to set the SQL mode before beginning the dump, so ANSI_QUOTES translation must be handled by my2pg instead.

10445 07/26/2013 06:35 PM Aaron Marcuse-Kubitza

bin/my2pg: comment out table options (http://dev.mysql.com/doc/refman/5.5/en/server-sql-mode.html#sqlmode_no_table_options) instead of removing them, because they include table COMMENTs, which contain important metadata such as table definitions. (note that table COMMENTs use a slightly different syntax than column COMMENTs, so the table COMMENTs will not be commented out twice.)

10444 07/26/2013 06:19 PM Aaron Marcuse-Kubitza

bin/my2pg: comment out COMMENTs instead of removing them so that they will be included in the PostgreSQL translation. COMMENTs contain important metadata about columns, such as definitions and the meanings of integer flag values.

10443 07/26/2013 05:58 PM Aaron Marcuse-Kubitza

inputs/{.,}*/*.schema.sql: regenerated using the instructions in bin/my2pg. this primarily replaces timestamp with text/*timestamp*/ (to preserve indefinite dates).

10442 07/26/2013 05:56 PM Aaron Marcuse-Kubitza

bin/my2pg: added instructions for regenerating *.schema.sql whenever this script is changed

10441 07/26/2013 05:22 PM Aaron Marcuse-Kubitza

bin/my2pg: COMMENT: also match COMMENTs with embedded ', because there will only be one COMMENT per line, so the contents of the COMMENT can just extend to the last ' on the line

10440 07/26/2013 05:16 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/util.sh: $sed_cmd: make output unbuffered, so that running e.g. bin/my2pg at the command line produces output as each line is read

10439 07/26/2013 04:29 PM Aaron Marcuse-Kubitza

bin/my2pg: replace MySQL ` quotes with " quotes to support exports that were generated without ANSI_QUOTES mode. (this replacement only applies to schema exports, not data.) ANSI_QUOTES is only available with mysqldump --compatible modes that also include NO_TABLE_OPTIONS, which omits important table options such as comments. in particular, these comments are part of schemas/VegCore/VegCore.ERD.mwb but were not being included in VegCore.my.sql.

10438 07/26/2013 01:41 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_string: removed parsed_taxon_assertion field, since there may be more than one parsing (TNRS result) for a given taxon_string. the parsing relationship can better be represented by adding a parsed_taxon_assertion whose taxon_assertion.string points to the parsed taxon_string. getting the parsed_taxon_assertion for a taxon_string now requires joining on parsed_taxon_assertion using a backwards instead of forwards fkey, and filtering the corresponding assertions to include only the ones for TNRS (of the desired TNRS version). documented that taxon_assertion.string was previously the concatenated matched name, but is now the TNRS input name. the concatenated matched name is still in parsed_taxon_assertion.matched_taxon_concept->:taxon_name.unique_name.

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