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Name Size Revision Age Author Comment
  _archive 1598 over 12 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 10016 over 11 years Aaron Marcuse-Kubitza added backups/vegbien.r9897.backup.md5
  bin 10023 over 11 years Aaron Marcuse-Kubitza bugfix: bin/make: need to leave bin/, ~/bin/ in...
  config 7801 over 11 years Aaron Marcuse-Kubitza root Makefile: VegBIEN DB: mk_db: Added command...
  exports 9928 over 11 years Aaron Marcuse-Kubitza added exports/_archive/
  inputs 10008 over 11 years Aaron Marcuse-Kubitza added inputs/GBIF/raw_occurrence_record_plants/...
  lib 10022 over 11 years Aaron Marcuse-Kubitza lib/sh/util.sh: command(): added nonrecursive=1...
  mappings 9882 over 11 years Aaron Marcuse-Kubitza mappings/VegCore-VegBIEN.csv: genus->taxonlabel...
  planning 9978 over 11 years Aaron Marcuse-Kubitza planning/workflow/bien3_architecture.pptx: stag...
  schemas 9991 over 11 years Aaron Marcuse-Kubitza schemas/VegBIEN/taxonomy/higherPlantGroup.xlsx....
  web 9997 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_ignore 30 Bytes 10002 over 11 years Aaron Marcuse-Kubitza /.rsync_ignore: added *.pyc
Makefile 12.5 KB 9917 over 11 years Aaron Marcuse-Kubitza bugfix: /Makefile: postgres-Linux: phpPgAdmin: ...
README.TXT 23.5 KB 10010 over 11 years Aaron Marcuse-Kubitza /README.TXT: Backups: TNRS cache: Back up/Resto...
fix_perms 97 Bytes 7560 over 11 years Aaron Marcuse-Kubitza Added root fix_perms
map 1001 Bytes 6949 almost 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
10023 06/25/2013 12:23 PM Aaron Marcuse-Kubitza

bugfix: bin/make: need to leave bin/, ~/bin/ in the PATH when running make nonrecursively, so that commands invoked by it which are located in these dirs (e.g. put, which will be used by `make inputs/upload`) can still be found. this requires using command()'s new nonrecursive=1 flag instead of running no_PATH_recursion, so that no_PATH_recursion() only affects the resolution of the command path, but does not propagate the filtered PATH to the invoked command itself.

10022 06/25/2013 12:18 PM Aaron Marcuse-Kubitza

lib/sh/util.sh: command(): added nonrecursive=1 flag, which uses cmd2abs_path to run an external command nonrecursively

10021 06/25/2013 12:16 PM Aaron Marcuse-Kubitza

lib/sh/util.sh: added cmd2abs_path, which makes the command in $1 nonrecursive

10020 06/25/2013 11:37 AM Aaron Marcuse-Kubitza

bugfix: lib/sh/util.sh: PATH_rm(): also need to remove adjacent occurrences of the same path (or occurrences which become adjacent when other paths are removed), which :...: matching wasn't doing because the trailing : is consumed, preventing it from being matched at the beginning of the next path. since unlike filesystem paths with /, it is not necessary for a match to span multiple :-separated sections, we can just use new split() to split apart the PATH into an array of paths, filter each path, and join() them back together.

10019 06/25/2013 11:33 AM Aaron Marcuse-Kubitza

lib/sh/util.sh: added split()

10018 06/25/2013 10:32 AM Aaron Marcuse-Kubitza

lib/sh/util.sh: auto-echo common external commands: added `which`

10017 06/25/2013 10:32 AM Aaron Marcuse-Kubitza

lib/sh/util.sh: auto-echo common external commands: use simpler echo_run instead of command since logging handling is not needed

10016 06/25/2013 08:50 AM Aaron Marcuse-Kubitza

added backups/vegbien.r9897.backup.md5

10015 06/23/2013 09:30 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: upload(): documented that each --include path is relative to the currdir, not the root dir of the upload ($local_dir). this feature, although previously unintended, is actually better because the user can change to a subdir of the root dir and specify upload paths relative to the dir they are in. however, when invoking upload() from a script with --include paths specified, this means you need to use an absolute path (e.g. "$(dirname "${BASH_SOURCE0}")"/...; or the value that will become $local_dir, which for sync_upload() is $root_dir).

10014 06/23/2013 08:56 PM Aaron Marcuse-Kubitza

backups/.rsync_ignore: replaced with .rsync_filter.upload to allow uploading new backups but not deleting existing backups if they don't exist on the local (rsync-invoking) side; and .rsync_filter.download to avoid downloading backups to the local side. this allows storing older backups just on jupiter, where there is much more disk space. note that this change must be made on the remote side (jupiter) for it to be effective, because these are remote-side rules and are only processed by the remote-side rsync instance.

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