mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: filter out genera that contain numbers (using new _filter_genus()), which break TNRS and prevent it from matching any other parts of the name. later, these genera can instead be moved to the end of the name, where TNRS will correctly match them as Unmatched_terms.

bugfix: inputs/VegBIEN/: added _no_import to disable import for this folder, since this is actually just an entry in web/datasources/ with VegPath redirection links, rather than an input to the import process. this fixes "schema "VegBIEN" does not exist" errors generated in `make test`.

inputs/input.Makefile: $(dontImport): also support putting a _no_import file at the top level in the datasource to exclude the entire datasource

bugfix: lib/sh/local.sh: removed make() override, which is no longer needed now that its operations are performed by verbosity_compat(), and which caused errors by setting $verbosity to the invalid value ""

bugfix: lib/sh/util.sh: verbosity_compat(): always use default verbosity (`unset verbosity`) when verbosity == 1, regardless of whether the caller has set $verbosity to the special value "", because $verbosity is supposed to be an integer field and "" is not supported by most functions that use $verbosity. in cases where a util.sh script is invoked, it will set $verbosity back to the default value 1, so this will function as before for util.sh scripts and fix $verbosity for scripts that use a different verbosity system.

added inputs/GBIF/raw_occurrence_record_plants/table.tsv.md5

inputs/GBIF/raw_occurrence_record_plants/test.xml.ref: regenerated. updated for new staging table input columns, which are now the same as the output columns.

bugfix: inputs/input.Makefile: %/VegBIEN.csv: use header from map.csv instead of the new columns, so that source.shortname is set to GBIF instead of VegCore

inputs/input.Makefile: %/VegBIEN.csv: when a runscript is available, instead map the output columns of map.csv to VegBIEN, because the columns have been renamed in the staging table

inputs/GBIF/raw_occurrence_record_plants/VegBIEN.csv: regenerated, which adds row_num input col

lib/sh/util.sh: echo_func(): check can_log at beginning of function, so that the resource-intensive func_loc (which calls `readlink -f`) does not need to be called if echo_cmd would not log anything at the current verbosity

lib/sh/util.sh: echo_func(): removed no longer used $minor flag. use `clog++... echo_func` instead.

lib/sh/util.sh: verbosity_compat(): don't make $verbosity a local var of this function, because then the changes will not be visible to the caller

bugfix: bin/make: use verbosity_compat because some make-invoked commands (e.g. bin/map) don't support verbosity=""

lib/sh/util.sh: command(): command__exec(): use verbosity_compat to support commands that don't support verbosity=""

lib/sh/util.sh: added verbosity_compat(), for use with commands that don't support verbosity=""

bugfix: lib/sh/local.sh: make(): when invoking overridden func, need make__make_sh

bugfix: lib/sh/util.sh: self, self_sys aliases: need to remove any func_override suffix __* from the FUNCNAME

bugfix: inputs/GBIF/import_order.txt, run: updated raw_occurrence_record/ to raw_occurrence_record_plants/

inputs/FIA/occurrence_all/test.xml.ref: update inserted row count

bugfix: bin/make: include local.sh so that its default verbosity-setting make() override will be used

lib/sh/local.sh: added make() override, which uses the default verbosity (i.e. verbosity="") when verbosity == 1. scripts that use lib/sql.py (which uses $verbosity) have different default verbosities, and this default should not be overriden by an env var, unless a higher verbosity has been set.

lib/sh/local.sh: added missing include of make.sh, used by root_make()

schemas/vegbien.sql: added _filter_genus()

inputs/GBIF/raw_occurrence_record_plants/run: import() runtime: specified that this does not include table.tsv.gz/make()

inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: Remove institutions that we have direct data for: # duplicates: added revision #

inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: Remove institutions that we have direct data for: documented that there are 4.5 million duplicates (59,998,354 rows before - 55,417,646 rows after = 4,580,708)

inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: Remove institutions that we have direct data for: added rerun time (~0 thanks to index, so no problem doing the DELETE each time postprocess.sql is run)

*{.sh,run}: use simpler .rel() instead of `. "$(dirname "${BASH_SOURCE<sup>0</sup>}")"/...` for relative includes

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

schemas/VegCore/VegCore.pg.sql: regenerated from installed schema. a Linux bug that caused constraints to be output in reverse order has now been fixed, as of 12.04.2 (broken in 12.04.1).

bugfix: inputs/GBIF/_MySQL/MySQL_schema, MySQL_data: sed: put {} commands on their own line to work on Mac

lib/sh/util.sh: .(): put echo_func on its own line for clarity

lib/sh/util.sh: .(): added echo_func (2 log_levels up because it's internal)

schemas/VegCore/mk_derived: use new lib/sh/local.sh instead of lib/import.sh (a precursor to util.sh, etc. still used by inputs/FIA/)

bugfix: load_data(): verbosity_min: use verbosity_min='' so that csv2db's default verbosity (3) is used, instead of setting the verbosity directly to 3, which caused the log++ logging output from bin/make to be echoed at verbosity 3, creating cluttered output

lib/sh/util.sh: verbosity_min(): support value '', which sets verbosity=''

bugfix: inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: updated column names to match the renamings in map.csv, which are now performed on the staging table itself

lib/sh/util.sh: run_args_cmd(): time the command so that the runtime of the outer runscript target (i.e. the command run from the shell) is printed at the end of the output, like in bin/make

bugfix: inputs/input.Makefile: %/install: don't run $(cleanup) if it has already been run by $(import_install_), so that it doesn't run twice

inputs/input.Makefile: %/postprocess: don't run postprocess.sql if it is supposed to be run by a runscript, because postprocess.sql may then depend on additional steps the runscript runs before it

lib/runscripts/table.run: import(): use self_make on load_data so that the remake status determines whether the table is reinstalled

bugfix: lib/runscripts/mysql.table.run: import(): added missing set_make_vars, needed by self_make

bugfix: lib/runscripts/table.run: load_data(): need to use $_remake instead of $remake when using set_make_vars

lib/runscripts/table.run: added set_make_vars to all make targets so $remake would be propagated appropriately

lib/runscripts/table.run: load_data(): also clobber install log if remaking, because the table will be reinstalled

lib/runscripts/table.run: load_data(): automatically select noclobber mode depending on whether the install log already exists. this removes the need for a separate load_data_first_run() function.

bugfix: lib/runscripts/table.run: load_data(): ignore errors if table already exists

lib/runscripts/table.run: load_data(): use noclobber=1 to avoid overwriting the install log when re-running the install target idempotently. load_data_first_run() is now available to preserve the output in the log on the first run.

inputs/input.Makefile: Staging tables installation: $(logInstall): don't output to the install log if $noclobber flag is set, to prevent overwriting the log when re-running the install target idempotently

bugfix: lib/runscripts/mysql.table.run: import(): move previous versions of table.tsv out of the main dir before loading staging tables, to prevent them from being considered a TSV segment file and prepended to table.tsv

lib/sh/util.sh: added mv2dir(), mv_glob which wrap mv

lib/sh/util.sh: added mkdir alias which adds -p to prevent errors if the dir already exists

lib/sh/util.sh: added wildcard alias, similar to make's $(wildcard) function

bugfix: inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: institution_code index: create it idempotently using create_if_not_exists() and an explicit index name, so that a duplicate index doesn't get added each time postprocess.sql is run

lib/sh/local.sh: psql(): don't put util in the search_path because psql scripts now add it themselves if they need it, using `SELECT util.search_path_append(util);`

inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: add util to the search_path so that postprocess.sql will also work when run by inputs/input.Makefile, which only puts the datasource (GBIF) in the search_path

schemas/util.sql: added search_path_append()

schemas/util.sql: added eval() to allow running EXECUTE outside of a function (and to echo the command that is run)

inputs/GBIF/raw_occurrence_record_plants/run: added import() runtime (5 h)

inputs/GBIF/raw_occurrence_record_plants/run: table.tsv.gz/make() runtime: noted that this excludes the upload time

inputs/GBIF/raw_occurrence_record_plants/run: added table.tsv.gz/upload() runtime (15 min)

added lib/runscripts/mysql.table.run (general to all MySQL datasources) and use it in inputs/GBIF/table.run

inputs/GBIF/raw_occurrence_record_plants/run: table.tsv/make(): to view runtime when using `screen`: keys used to scroll: added Ctrl-B/Ctrl-F for page-at-a-time scrolling (there are a lot of pages of output for the import() target!)

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

lib/sh/db.sh: set test mode when using limited # rows

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: lib/sh/sync.sh: also need to --include parent dirs for each --include path

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

*{.sh,run}: in comments, use ${array[@]} instead of @array for clarity

lib/sh/util.sh: foreach_arg(): moved `local a` to same line as for loop that uses it

bugfix: inputs/GBIF/table.run: table.tsv*/upload(): need to run put in live mode (live=1)

lib/sh/util.sh: foreach_arg(): echo_run the cmd at a log_level up so it isn't printed as if it were an external command (log_level 1)

lib/sh/sync.sh: removed `pf upload` debug statement

bugfix: lib/sh/util.sh: set_fds(): localize $i so it doesn't overwrite any previous value

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()

lib/sh/local.sh: added sync_upload(), sync_download() with $sync_local_dir, $sync_remote_url config vars

added lib/sh/sync.sh with upload(), download()

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

bugfix: lib/sh/util.sh: need to use `declare -p` instead of ${var+isset} because ${var+isset} returns not set for empty arrays

lib/sh/util.sh: added echo_vars() stub

lib/sh/util.sh: added echo_run() stub

lib/sh/util.sh: set_fds(): don't run (or echo) exec if no redirections are being made

bugfix: lib/sh/util.sh: added missing stub for indent alias (used by echo_func alias, which is a stub). without the stub, /usr/bin/indent would be used instead on Mac.

bugfix: lib/sh/local.sh: root_rel_path(): added echo_func

bugfix: lib/sh/local.sh: root_rel_path(): use canon_rel_path instead of rel_path because $1 may be absolute rather than relative to the current dir, so $root_dir needs to be absoluted (which requires $1 to be absoluted as well)

lib/sh/util.sh: support custom $base_dir, which will be run through realpath() to match $path ($PWD, which was used before, did not need to be realpath'd because it was already absolute)

lib/sh/util.sh: moved echo_func alias to stub because it must be embedded in its expanded alias form to work properly

lib/sh/util.sh: declare echo_func as a stub before it's defined, so that functions can use it even if they are defined before it (and its logging functionality will be enabled as soon as it's defined)

lib/sh/util.sh: rel_path(): don't log++ it, and instead only log++ applicable calls of it or its callers. this allows non-internal calls of rel_path() to be logged at the usual log_level.

lib/sh/local.sh: added root_rel_path()

lib/Firefox_bookmarks.reformat.csv: unescape HTML in page's description, such as links to more info. this is necessary to properly render the persistent shells link in the screen > scrollback folder description.

bin/repl: added unescape_html() filter function, which can be specified as the replacement string

bin/repl: support Unicode characters in the matched portion of the string

web/links/index.htm: updated to Firefox bookmarks. `screen`: scrollback: added link to our wiki page on persistent shells, which are a better way to support reconnecting.