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Name Size Revision Age Author Comment
  tapir 1670 over 12 years Aaron Marcuse-Kubitza bin/tapir/tapir2flat.php: Output to specieslink...
.rsync_ignore 13 Bytes 10004 over 11 years Aaron Marcuse-Kubitza added bin/.rsync_ignore with filters from /READ...
after_import 319 Bytes 14395 over 10 years Aaron Marcuse-Kubitza bin/after_import: use new bin/make_backups
autoremove 195 Bytes 4647 over 12 years Aaron Marcuse-Kubitza autoremove: `svn rm`: Fixed bug where needed to...
boldify 231 Bytes 11952 almost 11 years Aaron Marcuse-Kubitza bugfix: bin/boldify: also match [[]]-style link...
canon 1.36 KB 10283 over 11 years Aaron Marcuse-Kubitza bugfix: bin/*: spell out [:alnum:] as [a-zA-Z0-...
cat_cols 759 Bytes 4655 over 12 years Aaron Marcuse-Kubitza Added cat_cols
cat_csv 2.18 KB 3071 over 12 years Aaron Marcuse-Kubitza cat_csv: Support overwriting the existing heade...
cc_tty 133 Bytes 4421 over 12 years Aaron Marcuse-Kubitza Added cc_tty
ch_root 1.43 KB 3788 over 12 years Aaron Marcuse-Kubitza ch_root, ch_root_via: Documented that these are...
ch_root_via 712 Bytes 3788 over 12 years Aaron Marcuse-Kubitza ch_root, ch_root_via: Documented that these are...
collapse_multimap 683 Bytes 7444 almost 12 years Aaron Marcuse-Kubitza Added collapse_multimap, which collapses multim...
cols 639 Bytes 4662 over 12 years Aaron Marcuse-Kubitza cols: Support CSVs without a header, such as in...
count_error_rows 160 Bytes 1619 almost 13 years Aaron Marcuse-Kubitza count_error_rows: Allow input to be specified a...
csv2db 2.03 KB 7652 almost 12 years Aaron Marcuse-Kubitza csv2db: Open input stream in universal newlines...
db_dump_localize 501 Bytes 2617 over 12 years Aaron Marcuse-Kubitza db_dump_localize: Use new pg_version
debug2redmine 242 Bytes 3246 over 12 years Aaron Marcuse-Kubitza debug2redmine: Remove profiling information fro...
dict2redmine 3.68 KB 6838 about 12 years Aaron Marcuse-Kubitza dict2redmine: redmine_add_links(): Hyperlink ju...
digir_client 5.29 KB 1709 over 12 years Aaron Marcuse-Kubitza Moved parse_str() from xml_dom.py to xml_parse.py
disown_all 418 Bytes 1978 over 12 years Aaron Marcuse-Kubitza disown_all: Updated to use main function, local...
env_password 1.32 KB 1953 over 12 years Aaron Marcuse-Kubitza Scripts that are meant to be run in the calling...
error_stats 163 Bytes 960 almost 13 years Aaron Marcuse-Kubitza error_stats: Fixed to work on Mac
expand_braces 1.87 KB 3778 over 12 years Aaron Marcuse-Kubitza expand_braces: Fixed bug where needed to get ne...
expand_xpath 445 Bytes 1827 over 12 years Aaron Marcuse-Kubitza Added expand_xpath to expand XPath abbreviations
export_analytical_db 274 Bytes 8319 over 11 years Aaron Marcuse-Kubitza bin/export_analytical_db: Replaced analytical_a...
filter_errors 350 Bytes 3405 over 12 years Aaron Marcuse-Kubitza Always output Usage messages to stderr and word...
filter_errors_after 127 Bytes 1460 almost 13 years Aaron Marcuse-Kubitza Renamed bin/errors_filter_* to filter_errors_* ...
filter_errors_before 148 Bytes 1460 almost 13 years Aaron Marcuse-Kubitza Renamed bin/errors_filter_* to filter_errors_* ...
filter_out_ci 928 Bytes 10283 over 11 years Aaron Marcuse-Kubitza bugfix: bin/*: spell out [:alnum:] as [a-zA-Z0-...
filter_out_cs 829 Bytes 7033 almost 12 years Aaron Marcuse-Kubitza Added filter_out_cs
fix_line_endings 87 Bytes 8175 almost 12 years Aaron Marcuse-Kubitza Added bin/fix_line_endings to standardize \r\n ...
import_all 2.56 KB 14903 about 10 years Aaron Marcuse-Kubitza bin/import_all: converted to a runscript so it ...
import_date 547 Bytes 6974 about 12 years Aaron Marcuse-Kubitza import_date: Added note that Mac and Linux diff...
import_name 404 Bytes 6104 about 12 years Aaron Marcuse-Kubitza Added import_name, which gets the name of an im...
import_times 584 Bytes 10599 over 11 years Aaron Marcuse-Kubitza bugfix: bin/import_times: filtering out the Sou...
in_place 571 Bytes 13793 over 10 years Aaron Marcuse-Kubitza fix: bin/in_place: usage: removed duplicate cop...
ins_col 694 Bytes 4978 about 12 years Aaron Marcuse-Kubitza ins_col: Added column fill value param
invert 130 Bytes 3819 over 12 years Aaron Marcuse-Kubitza Added invert
jobspecs 232 Bytes 1545 almost 13 years Aaron Marcuse-Kubitza Added jobspecs to extract jobspecs (%#) from (p...
join 4.07 KB 7405 almost 12 years Aaron Marcuse-Kubitza join: Added support for direct mappings to VegB...
local_ip 232 Bytes 1677 over 12 years Aaron Marcuse-Kubitza Added local_ip to get local IP address
lockfile 1.41 KB 7430 almost 12 years Aaron Marcuse-Kubitza lockfile: Linux: Documented why newgrp and recu...
make 378 Bytes 14732 about 10 years Aaron Marcuse-Kubitza bugfix: bin/make: don't run verbosity_compat un...
make_analytical_db 751 Bytes 14644 over 10 years Aaron Marcuse-Kubitza schemas/public_.sql: viewFullOccurrence_*: rena...
make_backups 663 Bytes 14394 over 10 years Aaron Marcuse-Kubitza bugfix: bin/make_backups: need to `popd` when done
map 20.5 KB 11918 about 11 years Aaron Marcuse-Kubitza bugfix: bin/map: in_is_db: don't ignore errors ...
mk_rm_indexes 313 Bytes 3254 over 12 years Aaron Marcuse-Kubitza mk_rm_indexes: Also include the search_path in ...
mtime 275 Bytes 6968 about 12 years Aaron Marcuse-Kubitza Added mtime
my2pg 1.43 KB 10448 over 11 years Aaron Marcuse-Kubitza bin/my2pg: use s!...!...! when either the regex...
my2pg.data 488 Bytes 10237 over 11 years Aaron Marcuse-Kubitza bin/my2pg*: keep MySQL indefinite dates as text...
my2pg_export 330 Bytes 8274 over 11 years Aaron Marcuse-Kubitza bin/my2pg_export: Put --password first because ...
mysql_bien 188 Bytes 7577 almost 12 years Aaron Marcuse-Kubitza Added mysql_bien, which runs a MySQL command on...
name2pids 130 Bytes 7257 almost 12 years Aaron Marcuse-Kubitza Added name2pids
pg_dump_limit 207 Bytes 11870 about 11 years Aaron Marcuse-Kubitza bugfix: bin/pg_dump_limit: support errexit by i...
pg_dump_vegbien 818 Bytes 13161 over 10 years Aaron Marcuse-Kubitza lib/sh/db.sh pg_dump(), bin/pg_dump_vegbien: --...
pg_version 303 Bytes 2616 over 12 years Aaron Marcuse-Kubitza Added pg_version
pid2name 86 Bytes 7258 almost 12 years Aaron Marcuse-Kubitza Added pid2name
postgres_vegbien 211 Bytes 6949 about 12 years Aaron Marcuse-Kubitza vegbien_dest: Changed default $prefix to "", so...
profile_stats 360 Bytes 848 almost 13 years Aaron Marcuse-Kubitza Added profile_stats to analyze a profiling stat...
psql_script_vegbien 418 Bytes 7233 almost 12 years Aaron Marcuse-Kubitza psql_script_vegbien: Added no_query_results opt...
psql_vegbien 135 Bytes 6259 about 12 years Aaron Marcuse-Kubitza psql_vegbien: Run with sh because it no longer ...
psql_verbose_vegbien 329 Bytes 12394 almost 11 years Aaron Marcuse-Kubitza bin/psql_verbose_vegbien: use \\ instead of \ i...
publish_analytical_db 331 Bytes 8270 over 11 years Aaron Marcuse-Kubitza bin/publish_analytical_db: Fixed bug where need...
redmine_synonyms 787 Bytes 8233 over 11 years Aaron Marcuse-Kubitza mappings/Makefile: $(vocab); bin/redmine_synony...
reinstall_all 373 Bytes 11416 about 11 years Aaron Marcuse-Kubitza bin/*_all: *_main(): renamed to just main() bec...
remove_empty 298 Bytes 1284 almost 13 years Aaron Marcuse-Kubitza Added remove_empty to remove empty mappings in ...
repl 3.67 KB 13077 over 10 years Aaron Marcuse-Kubitza bin/repl: match as whole-word text (like SQL id...
reverse_join 330 Bytes 3405 over 12 years Aaron Marcuse-Kubitza Always output Usage messages to stderr and word...
review 1.87 KB 4788 over 12 years Aaron Marcuse-Kubitza review: Don't remove XML functions that are uni...
row 438 Bytes 3405 over 12 years Aaron Marcuse-Kubitza Always output Usage messages to stderr and word...
simplify_xpath 460 Bytes 611 almost 13 years Aaron Marcuse-Kubitza simplify_xpath: Be case sensitive to handle Veg...
sort 842 Bytes 727 almost 13 years Aaron Marcuse-Kubitza sort: Sort empty strings last so that inputs wi...
sort_ci 276 Bytes 7524 almost 12 years Aaron Marcuse-Kubitza Added sort_ci to sort a spreadsheet, ignoring l...
sort_filenames 834 Bytes 1658 over 12 years Aaron Marcuse-Kubitza Added sort_filenames to sort a list of filename...
sort_map 410 Bytes 3776 over 12 years Aaron Marcuse-Kubitza sort_map: Remove duplicates resulting from mult...
src_map 1.05 KB 10077 over 11 years Aaron Marcuse-Kubitza bin/src_map: support custom (or no) new_term_pr...
stop_imports 457 Bytes 13988 over 10 years Aaron Marcuse-Kubitza bugfix: bin/stop_imports: also need to include ...
sync_upload 101 Bytes 9892 over 11 years Aaron Marcuse-Kubitza added bin/sync_upload, a wrapper around sync_up...
tnrs_client 864 Bytes 14622 over 10 years Aaron Marcuse-Kubitza lib/tnrs.py single_tnrs_request(), bin/tnrs_cli...
tnrs_db 2.77 KB 14621 over 10 years Aaron Marcuse-Kubitza bin/tnrs_db: tnrs.tnrs_request() call: explicit...
translate 1006 Bytes 7448 almost 12 years Aaron Marcuse-Kubitza translate: Changed dictionary to thesaurus, sin...
translate_ci 354 Bytes 7434 almost 12 years Aaron Marcuse-Kubitza Added translate_ci
vegbien_dest 1.07 KB 12989 over 10 years Aaron Marcuse-Kubitza fix: bin/vegbien_dest: added public_validations
waitpid 247 Bytes 7262 almost 12 years Aaron Marcuse-Kubitza waitpid, lockfile: Changed $interval default to...
waitself 185 Bytes 7261 almost 12 years Aaron Marcuse-Kubitza Added waitself
with_all 1.01 KB 14089 over 10 years Aaron Marcuse-Kubitza bugfix: bin/with_all: isset(): need to use `&>/...
with_cat 339 Bytes 1449 almost 13 years Aaron Marcuse-Kubitza with_cat: Added support for custom cat command ...
with_cat_csv 217 Bytes 1450 almost 13 years Aaron Marcuse-Kubitza Added with_cat_csv
  • svn:ignore: dotlockfile

Latest revisions

# Date Author Comment
14903 10/26/2014 04:56 PM Aaron Marcuse-Kubitza

bin/import_all: converted to a runscript so it can use runscript functionality

14732 09/24/2014 07:23 PM Aaron Marcuse-Kubitza

bugfix: bin/make: don't run verbosity_compat until right before executing the external command, so that it doesn't mess up the logging mechanism. this is run automatically by command(), so there is no need to do anything here. note that logging bugs like these can now be troubleshooted much more easily with pst() to narrow down which functions could be causing the problem.

14644 09/04/2014 07:41 AM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.

14622 08/28/2014 08:13 PM Aaron Marcuse-Kubitza

lib/tnrs.py single_tnrs_request(), bin/tnrs_client: use_tnrs_export: default to False because this mode uses incorrect selected matches (vegpath.org/issues/943), and the JSON mode that fixes this is now available

14621 08/28/2014 08:05 PM Aaron Marcuse-Kubitza

bin/tnrs_db: tnrs.tnrs_request() call: explicitly set use_tnrs_export=True so that this continues to work if the default value is changed

14575 08/25/2014 09:13 PM Aaron Marcuse-Kubitza

bin/tnrs_client: added env var to configure use_tnrs_export

14443 08/09/2014 10:23 PM Aaron Marcuse-Kubitza

bin/make_analytical_db: materialize viewFullOccurrence_individual_view instead of analytical_stem_view because analytical_stem_view is now generatable via a simple join onto viewFullOccurrence_individual_view. this avoids running into potential disk space constraints when materializing and backing up both tables (~50 GB/table * 2 tables * 2 copies (incl. the backup) = 200 GB, which is very close to the available disk space).

14439 08/09/2014 09:52 PM Aaron Marcuse-Kubitza

bin/make_analytical_db: removed extra () around psql_verbose_vegbien

14438 08/09/2014 09:51 PM Aaron Marcuse-Kubitza

bin/make_analytical_db: removed no longer used mk_table()

14437 08/09/2014 09:49 PM Aaron Marcuse-Kubitza

bin/make_analytical_db: use more up-to-date *_view_modify() functions instead of mk_table()

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