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).
bugfix: inputs/GBIF/table.run: need to include lib/runscripts/mysql.table.run instead of table.run (table.run was accidentally substituted when inputs/.NCBI/table.run was copied to all new-style datasources
inputs/*/: added table.run for use by the table subdirs in new-style import. datasources without table subdirs do not need this.
added lib/runscripts/mysql.table.run (general to all MySQL datasources) and use it in inputs/GBIF/table.run
bugfix: inputs/GBIF/table.run: table.tsv.gz/make(): don't run table.tsv.gz/upload in test mode, to avoid clobbering the backup of a full table.tsv with a partial, testing table.tsv
bugfix: inputs/GBIF/table.run: table.tsv.gz/upload(): don't use inplace mode because it leaves a newer mtime when aborted, causing rsync to think that the partial upload is actually newer than the source. note that rsync's --partial-dir mode is just as capable of resuming an aborted upload (it will just use a file in .rsync-tmp instead). inplace mode is primarily designed for fixed-offset files which don't change much between edits, but this is not true for exports (or the gzips of them), which will change the file offsets of most data if even one row or column is added or removed.
bugfix: inputs/GBIF/table.run: table.tsv.gz/make(): run table.tsv.gz/upload here instead of in table.tsv/make() because it should not run until table.tsv.gz is finished being made, which is not the case in table.tsv/make() because table.tsv.gz/make is run in the background
inputs/GBIF/table.run: table.tsv.gz/upload(): moved before table.tsv.gz/make() so it can be used by it
bugfix: inputs/GBIF/table.run: table.tsv.gz/upload(): need overwrite=1 because the mtime of an aborted inplace upload is newer
inputs/GBIF/table.run: table.tsv*/upload(): renamed to table.tsv.gz/upload() to upload only table.tsv.gz, not table.tsv, in order to save bandwidth
bugfix: inputs/GBIF/table.run: table.tsv*/upload(): need to run put in live mode (live=1)
inputs/GBIF/table.run: table.tsv/make(): run table.tsv*/upload when the file make is done so that the file is backed up to jupiter
inputs/GBIF/table.run: added table.tsv*/upload()
inputs/GBIF/table.run: table.tsv/make(): remake table.tsv.gz/make() after table.tsv is made
inputs/GBIF/table.run: added table.tsv.gz/make()
lib/runscripts/subdir.run: auto-append -remake to all targets in remake mode
*{.sh,run}: make() calls: removed no longer applicable silent=1, which is now handled automatically by the log_level mechanism
inputs/GBIF/table.run: table.tsv.md5/make(): only use %-remake if remaking
bugfix: inputs/GBIF/table.run: table.tsv.md5/make(): use %-remake to ensure that the .md5 file is remade, regardless of the .md5 file's mtime relative to table.tsv. you would generally expect table.tsv's new mtime to be newer than the .md5 file's (thus triggering make to run), but if you e.g. ran svn up after making the table.tsv, this might not be the case.
inputs/GBIF/table.run: table.tsv/make(): use new set_large_table to prevent table.tsv from being deleted on error for full export runs (while still deleting it on error for sample subset runs)
bugfix: *run: overriding targets: use new self_make to properly progagate the $remake flag to the overridden target, so that the target itself is not skipped
bugfix: inputs/GBIF/table.run: table.tsv/make(): force table.tsv.md5 to be remade (using remake=1) because the table.tsv contents will have changed
lib/runscripts/table.run: include make.sh so runscripts based on it can use make-related utils
inputs/GBIF/raw_occurrence_record/run: moved table.tsv.md5/make() and invocation of it to inputs/GBIF/table.run because it's general to all tables (which would all use table.tsv for this datasource). use $target_filename in calling table.tsv.md5/make from table.tsv/make.
inputs/GBIF/raw_occurrence_record/run table.tsv/make() and functions used by it: added usage comments for cmd line usage, caller usage, and declaring function usage
inputs/GBIF/table.run: table.tsv/make(): use new mysql_export_local instead of ./MySQL_export
*{.sh,run}: removed extra space between function name and (), which is apparently not needed even though `help function` includes it. this greatly improves readability, including when function names are pasted into commit messages!
inputs/GBIF/table.run: table.tsv/make (): use echo_run instead of extern so that the command name is canonicalized properly
bugfix: : use new func_override for runscript inheritance instead of invoking the overridden function as a (command-line) target of the parent runscript. this ensures that the overridden function is run in the *same process as the calling function, so that $top_dir keeps the same value and runscript-relative paths continue to work.
lib/sh/util.sh: split make utils out into separate make.sh
inputs/GBIF/table.run: table.tsv/make (): use new to_target to auto-delete $target on error
inputs/GBIF/table.run: table.tsv/make (): use new check_target_exists
inputs/GBIF/table.run: table.tsv/make (): use extern so the MySQL_export command is echoed
inputs/GBIF/table.run: table.tsv/make (): don't make the target if it already exists
inputs/GBIF/table.run: table.tsv/make (): create the file directly rather than using inline_make, so that the command to create the file can use shell functions such as mysql
bugfix: inputs/GBIF/table.run: table.tsv/make (): need to use $(target) (target's path relative to curdir) instead of just the filename, now that make does not change the directory
inputs/GBIF/table.run: moved table.tsv creation to separate table.tsv/make () function
inputs/GBIF/table.run: renamed MySQL_export () to export_mysql () to match schemas/VegCore/VegCore.ERD.mwb.run
*{.sh,run}: changed echo_func to an alias that includes the "$", so that callers don't need to specify the "$" manually. although the original echo_func function is still there, callers need to switch over to the alias at the same time as it's defined because otherwise the "$@" would be doubled, since echo_func refers to the alias instead.
", so that callers don't need to specify the "$
moved lib/*.run into runscripts/ subdir so runscripts are grouped together and easier to find rather than being scattered throughout lib/
*run: added include guards
lib/util.run: inline_make (): pass Makefile commands using /dev/fd/3 (i.e. 3<<'EOF' ...) instead of stdin, to allow stdin to be used by commands that prompt the user
lib/util.run: echo_func (): use the caller's FUNCNAME via the $FUNCNAME[] array instead of requiring them to pass it in the function args as `echo_func "$FUNCNAME" "$@"`
inputs/GBIF/table.run: import(): Updated for lib/table.run template changes
*run: Use -e option to bash on the #! line instead of separate `set -o errexit` line so that there is no issue with the `set -o errexit` line getting separated from the #! line (errexit is required for the scripts to work properly)
lib/util.run: Run run_cmd at shell exit (using trap) instead of requiring every runscript to have `run_cmd ` at the end of it
Added inputs/GBIF/table.run
