lib/sh/util.sh: log!(): use new log:()

lib/sh/util.sh: added log:(), which sets an explicit log_level. this also simplifies log+().

lib/sh/util.sh: log+(): set log_level before PS4 so that the PS4 expr doesn't also need to add to log_level

lib/sh/util.sh: removed no longer needed log+ alias (which had been renamed from clog+)

lib/sh/util.sh: clog*: renamed to log* for clarity (possible now that log* is no longer used for function-local log_level setting)

: local setting of log_level: use log_local instead of relying on the log aliases, so that these aliases can instead be used for wrapping commands (the more common use case)

bugfix: lib/sh/util.sh: verbosity_compat alias: need to use `declare verbosity="$verbosity"` instead of `declare verbosity`, which would just clear $verbosity

bugfix: lib/sh/util.sh: verbosity_min alias: need to use `declare verbosity="$verbosity"` instead of log_local now that verbosity is not one of the vars changed by log++

lib/sh/util.sh: log+(): use easier-to-understand log_local instead of prefix-assignments to limit assignments to the invoked command

lib/sh/util.sh: log+(): use easier-to-understand log_local instead of prefix-assignments to limit assignments to the invoked command

: use clog instead of "log*"

bugfix: lib/sh/util.sh: log+(): removed spurious ; between setting of PS4 and log_level, which was causing erratic mismatches between PS4 and log_level. (the ; caused $PS4 to be set in the caller when invoked via one of the clog* aliases, rather than being passed as a command-specific env var.)

lib/sh/util.sh: $verbosity: stay constant at what the user set it to instead of changing in tandem with $log_level, to facilitate debugging verbosity/log_level-related issues

lib/sh/util.sh: log+(): usage: use aliases instead of ""-ed function names

added schemas/VegCore.ERD.pdf symlink for easy access

lib/sh/util.sh: log_err(): use red background for better visibility of errors, in the same way that lib/exc.py print_ex() does for column-based import

bugfix: lib/sh/util.sh: removed echo_func in functions used by log++, to avoid spurious highlighted output

lib/sh/util.sh: added missing clog+ alias

bugfix: lib/sh/util.sh: log_hint(): use the standard log_fd and log_info() format, not err_fd and log_err() format, for hint messages

fix: lib/sh/util.sh: log_msg!(): indent each line, not just the first

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

lib/sh/util.sh: log(): factored out helper function log_msg!()

fix: lib/sh/util.sh: highlight_msg(): bold instead of underlining because the underlining interferes with the readability of the commands

lib/sh/util.sh: highlight_msg(): allow turning off formatting w/ empty $format

fix: lib/sh/util.sh: log_err() calls: removed manual highlighting

lib/sh/util.sh: log_err(): highlight all error messages using highlight_msg()'s new $format

lib/sh/util.sh: highlight_msg(): support custom format

lib/sh/db.sh: pg_*_exists(): log the DB statements to check this at a higher log_level so that they don't clutter up the log output

lib/sh/util.sh: log(): highlight log_level 1 messages to stand out against other output, for easier debugging

*{.sh,run}: stderr_matches() wrapper calls: removed no longer needed prep_try/rethrow

bugfix: catch(): also need to support $1='' because this is a now a use case of ignore_e()

bugfix: lib/sh/util.sh: ignore_err_msg(): also need to ignore false exit status on no match

lib/sh/util.sh: stderr_matches(): moved prep_try/rethrow into the function itself so that callers don't have to wrap this function in a complex sequence of prep_try/rethrow statements

*{.sh,run}: stderr_matches() wrapper calls: removed no longer needed prep_try/rethrow

lib/sh/util.sh: stderr_matches(): moved prep_try/rethrow into the function itself so that callers don't have to wrap this function in a complex sequence of prep_try/rethrow statements

lib/sh/util.sh: added rethrow_exit alias

fix: lib/sh/db.sh: pg_table_exists(): use stderr_matches() rather than just the exit status. this also avoids highlighting the benign error.

fix: lib/sh/db.sh: pg_table_exists(): use stderr_matches() rather than just the exit status. this also avoids highlighting the benign error.

fix: inputs/input.Makefile: removed no longer used special handling of XML inputs, support for which was never added to the Makefile. (bin/map, however, does support importing an XML file into a database.) this fixes a bug in XAL, which used to abort with an error but now just imports an empty table.

fix: inputs/input.Makefile: %/install: don't ignore errors if table does not exist, to ensure a proper errexit. this is now possible because every dir that this target is being run on should be a data dir. (Source/ used to be a metadata-only dir.)

bugfix: inputs/input.Makefile: $(cleanup): need `set -o pipefail`

inputs/VegBank/run: `rm=1 import()`: updated runtime (1 h)

inputs/VegBank/taxon_observation.**/test.xml.ref: updated inserted row count

inputs/VegBank/projectcontributor_/test.xml.ref: updated inserted row count

bugfix: schemas/util.sql: is_constant(util.col_ref): updated to include standard newline at beginning of comment (applies to newly-imported staging tables)

bugfix: inputs/VegBank/import_order.txt: added missing project, needed to trigger the staging table renaming for the project table

inputs/VegBank/run: documented `rm=1 import()` runtime (>1.5 h)

inputs/VegBank/run: documented `datasrc_make sql/install` runtime (25 min)

inputs/MO/Specimen/test.xml.ref: updated, which adds dateCollected mappings

inputs/WIN/Specimen/test.xml.ref: updated to map.csv, which has eventDate->dateCollected

inputs/VegBank/plantconcept_/create.sql: updated runtime (25 min, ~same)

lib/sh/make.sh: begin_target: echo all targets to facilitate debugging without needing the verbose stack trace mode

bugfix: lib/sh/make.sh: echo_target: don't include filename/line #, since this is not for the stack trace mode

lib/sh/make.sh: added echo_target

*{.sh,run}: use new begin_target instead of `echo_func; set_make_vars`

lib/runscripts/util.run: runscript template: added sample make target, using new make target template

lib/sh/make.sh: added make target template

inputs/VegBank/plot/postprocess.sql: remove institutions that we have direct data for: CVS: updated runtime (same)

lib/sh/make.sh: added begin_target alias

lib/runscripts/datasrc_dir.run: documented how to reinstall staging tables (`rm=1 .../run import`)

bugfix: *{.sh,run}: stderr_matches() wrapper callers: use the required wrapper caller usage, which now includes rethrow and prep_try

bugfix: lib/sh/util.sh: rethrow*: only `return` if $e is actually nonzero, because rethrow is now being used as a catch-all in situations where there might not be an error

lib/sh/util.sh: prep_try: initialize $e to 0 to simplify error-handling coding

stderr_matches(): wrapper caller usage: added alternative usage when using `||`

lib/sh/util.sh: stderr_matches(): wrapper caller usage: documented usage for a negated condition (ie. prefixed w/ !)

lib/sh/util.sh: stderr_matches(): usage: split into wrapper usage and wrapper caller usage for clarity

fix: *{.sh,run}: stderr_matches() wrappers: usage: added `rethrow`

fix: *{.sh,run}: stderr_matches() wrappers: usage: added `rethrow`

fix: lib/sh/util.sh: stderr_matches(): usage: `rethrow` must be called right after stderr_matches(), to avoid calling running other commands if there is an error

fix: lib/sh/util.sh: stderr_matches(): when using $ignore_e, also set benign_error=1 to suppress the highlighting of the error

bugfix: lib/sh/db.sh: pg_schema_exists(): need to ignore benign error exit status from the "cannot create temporary relation in non-temporary schema" error

lib/sh/util.sh: stderr_matches(): supporting ignoring any benign error exit status associated with the error message being tested for

lib/sh/util.sh: stderr_matches(): usage: documented where any ignore_e statement would go

bugfix: lib/sh/util.sh: stderr_matches(): can't use `try` because this clears the exit status, which is needed for @PIPESTATUS to work. to support this, also need to avoid errexiting since @PIPESTATUS will be used instead.

lib/sh/util.sh: added dp(), which debug-prints a message

bugfix: inputs/VegBank/plot/postprocess.sql: use CVS.plot_ instead because that has the renamed staging table columns, and is compatible with auto-renaming of the SQL script columns

inputs/CVS/plot_/postprocess.sql: add unique constraint on locationName (analogous to the unique constraint in plot), for use by inputs/VegBank/plot/postprocess.sql in removing inter-datasource duplication

fix: schemas/util.sql: explain2notice_msg(): don't include EXPLAIN output for simple, single-value queries, to avoid cluttering up the log output

schemas/util.sql: added fold_explain_msg()

bugfix: bin/repl: only use excluded_prefix_re/excluded_suffix_re in text mode (used in renaming columns in SQL scripts), to prevent the special coding for column renames from also affecting regular regexp/word replacements

inputs/VegBank/taxon_observation.**/test.xml.ref: updated inserted row count

inputs/run: postprocess(): documented runtime (30 min)

bugfix: inputs/input.Makefile: %/postprocess.sql: don't perform replacements using map.csv, because map.csv is not idempotent. this functionality was only there to facilitate switching to new-style import, which is now largely done. (the remaining datasources NVS, SALVIAS, TEAM contain only 1 postprocess.sql: inputs/SALVIAS/projects/postprocess.sql (`st inputs/{NVS,SALVIAS,TEAM}/*/postprocess.sql`).)

bugfix: bin/repl: text mode: also don't match if it's part of a '-'-separated identifier

bugfix: bin/repl: text mode: also don't match if it's a word in a sentence

bugfix: bin/repl: text mode: turned off the suffix matching, because there are cases where a mapping adds a suffix which would cause the same replacement to be performed repeatedly

inputs/input.Makefile: %/postprocess.sql: always run this, not just if the associated map spreadsheets change, to avoid needing to `touch` them to cause %/postprocess.sql to run

bin/repl: text mode: exclude prefixes that should not cause replacement, to avoid doubling leading *

fix: inputs/*/*/postprocess.sql: un-doubled *

bugfix: inputs/input.Makefile: %/postprocess.sql: also need to apply renames from mappings/VegCore.thesaurus.csv, as these have been applied to map.csv

bugfix: lib/runscripts/table.run: custom_postprocess(): need to apply renames to SQL statements in postprocess.sql before it can be run

bin/repl: text mode: also match w/ suffix (eg. _verbatim)

bugfix: /README.TXT: Maintenance: VegCore data dictionary: apply new data dict mappings: need to use postprocess rather than import runscript target, so that the command also works on an svn checkout without the flat files (the flat files are not needed for the staging table renaming)

lib/sh/db.sh: psql(): $verbose_ok: renamed to $bypass_ok for clarity, because this applies only to the `--output /dev/fd/41` bypass (which when not possible, requires turning off verbose output

fix: lib/sh/db.sh: psql(): added $output_data switch analogous to what mysql() has. this causes query results of eg. void-returning functions to be correctly filtered by the logging mechanism, rather than output to stdout.

fix: lib/sh/db.sh: psql(): verbosity=0 (errors only) mode: use `SET client_min_messages = WARNING;` instead of NOTICE to hide verbose messages within psql as well

lib/sh/db.sh: psql(): replaced `test "$verbose_ok" && can_log` with bool var $verbose_

fix: lib/sh/db.sh: psql(): $verbose_: renamed to $verbose_ok for clarity

fix: lib/sh/util.sh: stdout_contains(): add another pipe_delay because the `grep` statement was sometimes getting printed before its filtered output

bugfix: schemas/util.sql: set_col_types(): need to COALESCE the executed SQL to '' because util.eval() does not support NULL (and shouldn't, because this indicates a missing COALESCE in constructing the statement)