schemas/vegbien.sql: place.geovalid: require it to be NOT NULL so that it's always a 2-valued boolean (but default it to false since it's not a required field)

mappings/VegCore-VegBIEN.csv: place.geovalid: use false instead of NULL

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): exclude deleted rows (i.e. where the deleted timestamp is non-NULL)

inputs/GBIF/raw_occurrence_record/header.csv: regenerated using ./run. since the table is reimported as a CSV, it uses bin/csv2db, which prepends an additional row_num column.

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): remove explicit cols list to include all cols. the file size of the generated table.tsv will increase by ~3x, but should remain reasonably-sized compared to our available disk space.

bugfix: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): need \ line continuation after vars so they only apply to the command rather than being set as global vars

bugfix: lib/runscripts/table.run: load_data(): use new $verbosity_min instead of running `verbosity_min` so that the command name logging is not output with the new verbosity

lib/sh/util.sh: added $verbosity_min to set a `verbosity_min` value after the command name, etc. has been logged, so that the logging itself is not output with the new verbosity

schemas/vegbien.sql: range_modeling_input: include only plants (i.e. rows with higher_plant_group IS NOT NULL)

schemas/vegbien.sql: range_modeling_input: added higher_plant_group, for use in restricting rows to plants

inputs/.geoscrub/geoscrub_output/map.csv: *validity: added definitions of the numeric codes from _src/README.TXT

added planning/workflow/validation/GeoDistKM.sql.txt

planning/goals/BIEN3_derived_data_products.docx: updated to most recent version from Brad's e-mail on 2013-4-16

/README.TXT: Full database import: before running screen: added `unset TMOUT` because TMOUT (autologout) causes screen to exit even with background processes active

/README.TXT: Maintenance: added things to put in your .profile on a live machine (e.g. vegbiendev). in particular, you MUST NOT have a TMOUT (autologout) set, because this causes screen to exit even if background processes (e.g. from column-based import) are running

/README.TXT: Maintenance: added things to put in your .profile on a live machine (e.g. vegbiendev). in particular, you MUST NOT have a TMOUT (autologout) set, because this causes screen to exit even if background processes (e.g. from column-based import) are running

bugfix: lib/runscripts/table.run: load_data(): need to ensure the verbosity is at least 3 because the install logs require verbose output. (3 is the default for the installer, but is overridden by the runscripts, which instead set the default to 1.)

lib/sh/util.sh: logging: added verbosity_min()

lib/sh/util.sh: logging: added verbosity_int() and use it instead of `round_down "$verbosity"`

bugfix: lib/sh/util.sh: log+ alias: don't expand next word because it's not a cmd

lib/runscripts/table.run: $schema, $table: log the `cd` used to calculate the value at log_level 3 instead of 1 (note that the cd() function call for this will be logged at log_level 5)

lib/sh/util.sh: cd(): trace-log the cd() function call itself (at log_level 3) in addition to the cd builtin call

lib/runscripts/table.run: import(): added step to load the data into the staging table before postprocessing it

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.

bugfix: lib/sql.py: parse_exception(): typed_name_re: need to ensure that full name is matched rather than just first character

web/links/index.htm: updated to Firefox bookmarks. Mountain Lion upgrade: added Python psycopg2, Python OrderedDict, X11.

lib/runscripts/table.run: table_make(): run canon_rel_path on the datasrc dir so it's displayed as the direct path to it, without ..

lib/runscripts/table.run: table_make(): moved comment about "${@/#/$table/}" to right after the line it describes

lib/runscripts/table.run: input_make(): renamed to table_make() to make it clear that the target names are relative to the table subdir itself, not the datasrc dir. it was previously called input_make because it used inputs/input.Makefile directly, but now will use any Makefile in the datasrc dir.

added inputs/GBIF/Makefile, which links to ../input.Makefile, to allow running make directly in the datasrc dir (i.e. without --makefile=.../input.Makefile). this is required by the runscripts.

inputs/GBIF/raw_occurrence_record/run: table.tsv.md5/make(): don't add extra .md5 extension to $target_filename because it already has the extension as part of the target name (now that this command is run in its own make target rather than in table.tsv/make())

lib/sql_gen.py: import OrderedDict from collections instead of ordereddict for Mac 10.8 Mountain Lion upgrade

lib/sh/util.sh: logging: renamed $log_level_indent to $log_indent_step to avoid confusion with the log_level, which is a different kind of indent (using + signs instead of |s)

lib/sh/util.sh: logging: also export PS4, because it follows verbosity and therefore also needs to be propagated to invoked commands

lib/sh/util.sh: can_log(): support decimal verbosities using round_down()

lib/sh/util.sh: always use echo_export instead of export, even when the verbosity at load time would suppress output, because the verbosity may actually increase during the script due to log-- calls, etc., and vars should then still be echoed as expected

lib/sh/util.sh: log+: inlined PS4_prefix_n alias because there is now room for it

lib/sh/util.sh: log+: $verbosity: support decimal verbosities (but not decimal log_levels) by using new float+int

lib/sh/util.sh: removed no longer used log-. use log+ with a negative argument instead.

bugfix: lib/sh/util.sh: log+: PS4 when $1 < 0: need to negate $1 because now it's a negative number

lib/sh/util.sh: log--: use log+ with 1 instead of log so we don't need a separate log- function

lib/sh/util.sh: logging: log+: support negative log_level adjustments. log-: use log+ with the negative of its argument

web/links/index.htm: updated to Firefox bookmarks. sorted MySQL and PostgreSQL sections.

web/links/index.htm: updated to Firefox bookmarks

web/links/index.htm: Mac 10.8 Mountain Lion > PostgreSQL: appended tab to name to disambiguate it from the general PostgreSQL section

bugfix: web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name: also renamed the corresponding self-anchor hyperlinks

bugfix: web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name: need to replace all occurrences (using /g option to sed) to include both HTML anchors on the line

web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name

lib/sh/util.sh: sed: changed it to an alias so it will also be expanded when passed to an external command (like in_place) that can only run an executable, not a shell function (this occurs as long as the external command is defined as an alias which ends in space, to alias-expand the next word). added associated $sed_cmd var for cases when there is no alias wrapper around the external command, and the literal alias body must be used instead.

lib/sh/util.sh: log+/-(): setting verbosity: added space around operators to support negative numbers

lib/sh/util.sh: added float functions (esp. float+int()) for dealing with decimal verbosities used by sql.py and column-based import

inputs/GBIF/raw_occurrence_record/run: inputs/GBIF/raw_occurrence_record/run: added check_target_exists so you know why make skipped the file (for other, non-silent targets, it would also avoid make's verbose output when the file exists)

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): moved making of table.tsv.md5 to separate function

lib/sh/util.sh: $log_fd: indicated that this is only initially stderr (however, the new port will just use stderr if it's not redirected separately)

lib/sh/util.sh: verbosities: 3: added that this includes values of kw params

lib/sh/util.sh: logging: added description of the verbosities available, including what each one does and what it's useful for:

1. verbosities:
2. 0: just print errors. useful for cron jobs.
3. 1: also external commands run. useful for running at the command line....

lib/sh/util.sh: command__set_fds(): echo the >& line at a higher log_level, because this information (i.e. which fd is used by the command for logging) is primarily for debugging and should not normally be printed

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): also add md5 sum for table.tsv

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): added back filter kw args, which had gotten deleted in a commit without update (although actually, svn should not allow a commit without update, so the working copy may have gotten corrupted)

lib/runscripts/table.run: input_make(): added $silent flag which turns on make's --silent option

lib/sh/make.sh: set_make_vars: usage: added "use $target" to indicate that vars are made available by this alias

lib/sh/make.sh: inline_make(): take the script stdin from caller-provided stdin and get make's stdin from global stdin, so that the caller can just use <<'EOF' rather than having to include a specific fd before the <<

lib/runscripts/table.run: input_make(): documented that it requires a Makefile in the datasrc dir containing `include ../input.Makefile

lib/runscripts/table.run: input_make(): added comment explaining that "${@/#/$table/}" replaces the empty str at the beginning of str (/#) with $table/

lib/runscripts/table.run: put functions on one line where possible

lib/runscripts/table.run: input_make(): use the local make() function instead of external make directly, because it sets $cmd_log_fd appropriately to ensure that all the echoed make commands get properly logged to stdlog/stderr (stdlog is fd 30 when it's redirected to a file)

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

web/links/index.htm: updated to Firefox bookmarks

web/links/index.htm: updated to Firefox bookmarks

web/links/index.htm: removed no longer needed - at the beginning of every folder's description

lib/Firefox_bookmarks.reformat.csv: label page's description: don't do this for folders (i.e. descriptions preceded by an <H3> tag) because their descriptions are always author-added rather than from a web page. this avoids needing to add a - at the beginning of every folder's description.

web/links/index.htm: updated to Firefox bookmarks. upgrading Mac OS X to 10.8 Mountain Lion: put fixes subdirs in order.

web/links/index.htm: updated to Firefox bookmarks. upgrading Mac OS X to 10.8 Mountain Lion: put fixes subdirs in order.

web/links/index.htm: updated to Firefox bookmarks. upgrading Mac OS X to 10.8 Mountain Lion: added fixes for Apache ~/Sites dirs, Apache PHP

web/links/index.htm: updated to Firefox bookmarks. added bookmarks for upgrading Mac OS X to 10.8 Mountain Lion. (WARNING: DO NOT upgrade unless you are prepared to fix several programs broken by the upgrade: svn, PostgreSQL. instructions are in the corresponding bookmark subdirs. these programs will be COMPLETELY UNAVAILABLE until they are manually fixed!)

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): cols: also include scientific_name, which is preferable as a TNRS input because it also contains lower ranks

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): cols: also include id, institution_code, collection_code, catalogue_number

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): added filter for institution_codes in herbaria.ih (in PostgreSQL)

inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): added column subset (from http://vegpath.org/twiki/bin/view/Main/ConfCall20130509#subsetting_strategy > include)

lib/sh/db.sh: mk_select: constructed queries: in ${var:+if_true} syntax, put the newline at the end of the if_true value instead of the beginning, so that each ${var:+if_true} expression starts at the beginning of a line

lib/sh/db.sh: mk_select: constructed queries: support custom columns list using $cols

lib/sh/db.sh: mk_select: constructed queries: support WHERE clause using $filter

lib/sh/util.sh: echo_stdin(): don' increase the log_level, because the input being sent to the command (which is usually a set of interpreted commands itself) is necessary to fully know what action is being performed

bugfix: lib/sh/local.sh: add a manual errexit for $() exprs by embedding them in just a var assignment (without local or declare), whose exit status will then equal the of the $(). a `|| return` also needs to be added because errexit does not work on assignment statements. this commit adds them for func_loc(), echo_func(), canon_rel_path(), set_paths(), save_cache, cached realpath(), local.sh global vars

lib/sh/util.sh: shell-variable-based caching: usage: updated alias names

web/links/index.htm: updated to Firefox bookmarks. regenerating also removed extra <a name=...> tags that were added when running index.htm.run on an already-processed index.htm.

bugfix: lib/sh/util.sh: `set -o`: need a -o before every option to set

lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links' names: hyperlink the added anchors as clickable paragraph marks (like Redmine), which take you to the HTML anchor. this is analogous to the clickable folder names which take you to their anchors.

lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links' names, in addition to their URLs

bugfix: lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links' URLs: use .*? instead of .* to match the contents of the <A> tag before the HREF

lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links using the URL itself as the anchor. these can be used to link to the comments attached to a bookmark in the bookmarks page, rather than to the bookmark's destination.

lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links using the URL itself as the anchor. these can be used to link to the comments attached to a bookmark in the bookmarks page, rather than to the bookmark's destination.

web/links/index.htm: updated to Firefox bookmarks

lib/sh/util.sh: `set -o`: added pipefail option, to ensure that exit statuses (esp. for errexit) also work with pipelines (a|b)

lib/sh/util.sh: use new log+ with a numeric arg instead of multiple calls to log++

lib/sh/util.sh: use new log+ with a numeric arg instead of multiple calls to log++. use the command form of log-- (`log-- echo_func`) to counter the normal log++ performed by echo_func, for cases when the function name is descriptive and should be output at the same log_level as the commands it runs.

*{.sh,run}: removed extra space between function name and ()

lib/sh/util.sh: echo_func(): take the FUNCNAME as an argument (auto-added in the echo_func alias) instead of getting it from the FUNCNAME array (which would have produced an inaccurate value if another function call (such as log++) intervened between the caller and echo_func())

lib/sh/util.sh: echo_func(): display where the function was declared (using new func_loc()) instead of where echo_func() was called from. this is more intuitive when debugging, becaues the line # is where the function starts. it also helps remove the dependency on the FUNCNAME/BASH_* arrays, which would produce an inaccurate value if another function call (such as log++) intervened between the caller and echo_func().

lib/sh/util.sh: added func_loc(), which gets where a function was declared in the format file:line, and helper alias set_func_loc