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root/trunk/bin @ 12701

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 472 Bytes 11429 about 11 years Aaron Marcuse-Kubitza bin/after_import: support turning off the end-o...
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 1.71 KB 11839 about 11 years Aaron Marcuse-Kubitza bin/import_all: don't import NCBI because the l...
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 424 Bytes 8735 over 11 years Aaron Marcuse-Kubitza bin/in_place: set the permissions of the new fi...
ins_col 694 Bytes 4978 over 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 435 Bytes 10066 over 11 years Aaron Marcuse-Kubitza bin/make: moved $make_filter_active test to lib...
make_analytical_db 1.5 KB 12391 almost 11 years Aaron Marcuse-Kubitza bin/make_analytical_db: added `public_validatio...
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 809 Bytes 12041 almost 11 years Aaron Marcuse-Kubitza bugfix: bin/pg_dump_vegbien: fixed arg-count ch...
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 2.34 KB 10348 over 11 years Aaron Marcuse-Kubitza bugfix: bin/repl: text mode: repurpose this to ...
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 almost 13 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 432 Bytes 1953 over 12 years Aaron Marcuse-Kubitza Scripts that are meant to be run in the calling...
sync_upload 101 Bytes 9892 over 11 years Aaron Marcuse-Kubitza added bin/sync_upload, a wrapper around sync_up...
tnrs_client 750 Bytes 9520 over 11 years Aaron Marcuse-Kubitza lib/tnrs.py: repeated_tnrs_request(): renamed t...
tnrs_db 2.72 KB 10742 over 11 years Aaron Marcuse-Kubitza bin/tnrs_db: add entry to new batch table
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 1.05 KB 8183 almost 12 years Aaron Marcuse-Kubitza schemas/*functions.sql: Renamed to *util.sql be...
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 953 Bytes 11456 about 11 years Aaron Marcuse-Kubitza bugfix: bin/with_all: @inputs default value: us...
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
12394 02/23/2014 08:29 PM Aaron Marcuse-Kubitza

bin/psql_verbose_vegbien: use \\ instead of \ inside '' because this is sh, not bash
12393 02/23/2014 08:26 PM Aaron Marcuse-Kubitza

bin/psql_verbose_vegbien: changed prep-statement order to match lib/sh/db.sh psql()
12392 02/23/2014 08:26 PM Aaron Marcuse-Kubitza

bin/psql_verbose_vegbien: use `\set VERBOSITY terse` to hide stack traces/DETAIL sections of error messages, like in lib/sh/db.sh psql()
12391 02/23/2014 08:11 PM Aaron Marcuse-Kubitza

bin/make_analytical_db: added `public_validations.remake_diff_tables()`
12041 02/05/2014 12:55 AM Aaron Marcuse-Kubitza

bugfix: bin/pg_dump_vegbien: fixed arg-count check to allow passing command-line options to pg_dump via args
11970 01/20/2014 11:33 AM Aaron Marcuse-Kubitza

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).
11952 01/15/2014 08:16 AM Aaron Marcuse-Kubitza

bugfix: bin/boldify: also match [[]]-style links at the beginning and end of a line
11951 01/15/2014 08:11 AM Aaron Marcuse-Kubitza

bin/boldify: made it idempotent
11950 01/15/2014 08:08 AM Aaron Marcuse-Kubitza

bugfix: bin/boldify: fixed extended regular expression syntax, which doesn't support a \] inside [] (you instead have to put the ] right after the opening [^ )
11949 01/15/2014 07:59 AM Aaron Marcuse-Kubitza

added bin/boldify, which makes Redmine links bold

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