bin/in_place: diff: use --brief to avoid scanning the entire file for large files

bin/in_place: added $preserve_mtime flag

lib/sh/db.sh pg_dump(), bin/pg_dump_vegbien: --format: use the long form of the formats to make the code self-documenting

bin/repl: match as whole-word text (like SQL identifier): documented that this is a generalization of lib/sql_gen.py map_expr() to work on entire source files

bin/repl, lib/sql_gen.py Expression transforming: documented that this can also be done in Postgres with expression substitution (wiki.vegpath.org/Postgres_queries#expression-substitution)

bin/make_analytical_db: removed remake_diff_tables() because this is now done for each datasource in inputs/input.Makefile

bin/make_analytical_db: removed no longer needed "${public}_validations" schema qualifier, now that it is in the search_path

fix: bin/vegbien_dest: added public_validations

fix: bin/repl: text mode (whether all patterns are plain text) should default to on, not off, if matching entire cells in a spreadsheet

fix: bin/repl: don't consider uppercase SQL keywords to indicate that a word is in a sentence

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

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

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

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

bin/psql_verbose_vegbien: use \\ instead of \ inside '' because this is sh, not bash

bin/psql_verbose_vegbien: changed prep-statement order to match lib/sh/db.sh psql()

bin/psql_verbose_vegbien: use `\set VERBOSITY terse` to hide stack traces/DETAIL sections of error messages, like in lib/sh/db.sh psql()

bin/make_analytical_db: added `public_validations.remake_diff_tables()`

bugfix: bin/pg_dump_vegbien: fixed arg-count check to allow passing command-line options to pg_dump via args

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: bin/boldify: also match [[]]-style links at the beginning and end of a line

bin/boldify: made it idempotent

bugfix: bin/boldify: fixed extended regular expression syntax, which doesn't support a \] inside [] (you instead have to put the ] right after the opening [^ )

added bin/boldify, which makes Redmine links bold

bugfix: bin/map: in_is_db: don't ignore errors when the table does not exist, because these prevent an errexit and allow an import to continue when a staging table is missing. suppressing this error had previously been necessary because metadata-only tables (Source/) used to not have installed staging tables, and the program had to react accordingly.

bugfix: bin/pg_dump_limit: support errexit by ignoring the nonzero exit status that grep returns when it doesn't match anything

bin/make_analytical_db: don't regenerate family_higher_plant_group from the NCBI data because the lookup table is now prepopulated as part of the schema

bin/import_all: don't import NCBI because the lookup table is now prepopulated as part of the schema

bugfix: bin/import_all: run in errexit mode, so that if the user cancels reinstalling of the import schema, the script will then abort instead of continuing and using the wrong schema

bin/map: support param start="", which indicates the default value. this fixes a bug in inputs/input.Makefile $(restart_row), which outputs "" if an explicit starting row is not found.

bugfix: bin/with_all: @inputs default value: use `local`, so that the default value is only set for the current function and doesn't leak back out into the caller. this fixes a bug in subset imports where import_all's Source/import call to with_all would add the .* datasources, but these would then stay in for the import_scrub call, causing extra .* datasources to incorrectly be imported.

bin/make_analytical_db: removed no longer needed setting of $schema to $public, because this is now done by psql()

bugfix: bin/import_all: restore the working dir when main() is done, in case it started as something other than the root dir

bin/after_import: support turning off the end-of-import backup for imports that are not the full database

bugfix: bin/make_analytical_db: when running into a public schema other than "public", also pass this to `/run export_` (which currently uses $schema instead of $public)

bugfix: bin/import_all: fix $ when .-included without args (which causes bash to put the wrong values in $ instead of leaving it empty)

bin/import_all: `make schemas/$version/install`: reinstall instead to allow re-running the import to the same custom schema (e.g. 2013-10-18.Brian_Enquist.Canadensys)

bin/import_all: `make schemas/$version/install`: ignore errors if schema exists, to support running with -e

bugfix: bin/import_all: removing inputs/.TNRS/tnrs/tnrs.make.lock: use `"rm" -f` instead of plain "rm" to avoid having an error exit status, which will abort the script if run with the -e flag (as runscripts are)

bin/*_all: *_main(): renamed to just main() because it does not matter that other shell-includes' main() methods will clobber this, because it is only executed once

bugfix: bin/import_all: Source tables: use .../import instead of import_temp because import_temp is only needed when importing all tables, to prevent the temp suffix from being removed yet

fix: bin/map: put template: comment out the "Put template:" label so that the output is valid XML, and displays properly in a browser rather than showing a syntax error

bugfix: bin/import_all: need to publish datasources that won't be published by `make .../import`, so that the per-datasource import XPaths that refer to TNRS/geoscrub will link up with the TNRS/geoscrub source entry instead of creating a new entry without the metadata (because the entry with the metadata was named TNRS.new/geoscrub.new)

bin/import_all: removed no longer needed import of geoscrub data, because analytical_stem_view is now joined to the geoscrub_output table directly, instead of using the imported canon_place entries

bin/with_all: $all: renamed to $hidden_srcs for clarity, since this now just adds the hidden (.*) datasources, rather than always using all datasources

bugfix: bin/with_all: in $all mode, just prepend the .* datasources to the user-selected (or default) @inputs, so that using $all to add these datasources doesn't inadvertently cause the action to be performed for all datasources

bin/import_all: usage: documented that this can now be run with a custom datasources list (each of the form inputs/src/)

bin/with_all: added support for providing a custom list of inputs to run the command on

bin/import_all: use just import_scrub, not reimport_scrub, because import_scrub now automatically publishes the datasource's import (i.e. removes the temp suffix)

bin/map: usage: documented that verbosity > 3 in commit mode turns on debug_temp mode, which creates real tables instead of temp tables

bugfix: bin/import_all: use reimport_scrub instead of import_scrub so that the temp suffix of the datasource name is removed

bugfix: bin/after_import: run backups/fix_perms right after the backup files are created to make them private

bugfix: bin/make_analytical_db: `/run export_`: don't take input from the terminal, because this causes rm to prompt the user (from a background task) about overwriting the previous export

bin/map: allow user to override the source env var, which is used as the source.shortname value in the DB

bugfix: bin/import_all: `rm inputs/.TNRS/tnrs/tnrs.make.lock`: need to use `"rm"` instead of `rm` so that we don't use any rm alias the user might have in their shell (import_all is run in the calling shell so that the jobs are owned by the calling shell)

bin/import_all: added step to remove any leftover TNRS lockfile (previously done manually)

bin/tnrs_db: add entry to new batch table

bugfix: bin/import_times: filtering out the Source subdirs: need to match 1 at the beginning of the line only

bin/import_times: filter out the Source subdirs, which now have single-row data and therefore are included in the rowcounts list

bin/after_import: usage: documented that it requires $version

bin/import_all: use new bin/after_import

added bin/after_import, which performs post-normalized-import actions separately from bin/import_all

bin/import_all: with_all import_scrub: documented that this step uses $by_col, so that users know to include by_col=1 when running this step separately

bin/import_all: use column-based import (by_col=1) by default, instead of requiring the user to explicitly specify it. instead turn it off explicitly (by_col=) for row-based import.

bin/import_all: don't set $dump_opts until running the backup command that uses it, so that the user can run this backup command separately just by copying the line out of the script (without worrying about env vars that need to be set, other than $version which is visible outside the script)

bin/my2pg: use s!...!...! when either the regexp or the replacement contains / , to avoid unnecessary \-s

bin/my2pg: commenting out table options: added explanatory comment, because it is not obvious from the regexp what this does

bin/my2pg: comment out table options (http://dev.mysql.com/doc/refman/5.5/en/server-sql-mode.html#sqlmode_no_table_options) instead of removing them, because they include table COMMENTs, which contain important metadata such as table definitions. (note that table COMMENTs use a slightly different syntax than column COMMENTs, so the table COMMENTs will not be commented out twice.)

bin/my2pg: comment out COMMENTs instead of removing them so that they will be included in the PostgreSQL translation. COMMENTs contain important metadata about columns, such as definitions and the meanings of integer flag values.

bin/my2pg: added instructions for regenerating *.schema.sql whenever this script is changed

bin/my2pg: COMMENT: also match COMMENTs with embedded ', because there will only be one COMMENT per line, so the contents of the COMMENT can just extend to the last ' on the line

bin/my2pg: replace MySQL ` quotes with " quotes to support exports that were generated without ANSI_QUOTES mode. (this replacement only applies to schema exports, not data.) ANSI_QUOTES is only available with mysqldump --compatible modes that also include NO_TABLE_OPTIONS, which omits important table options such as comments. in particular, these comments are part of schemas/VegCore/VegCore.ERD.mwb but were not being included in VegCore.my.sql.

bugfix: bin/repl: text mode: repurpose this to match SQL identifiers, for use by inputs/input.Makefile %/postprocess.sql. %/postprocess.sql is the only place currently using this mode, so this will not affect other scripts.

bugfix: bin/*: spell out [:alnum:] as [a-zA-Z0-9] because Python unfortunately doesn't support character classes

bin/*: replaced confusing regexp constructs involving \W inside [] with the much clearer explicit character class [:alnum:] . this avoids adding or subtracting from an inverted class in order to reach a subset of the corresponding positive class, because the subset can just be named explicitly instead.

bugfix: bin/repl: doesn't make sense to use other chars in a [^\W_] regexp, because they will have no effect since \w doesn't include the other chars to begin with. this is a result of confusion with the ^ and \W double negative.

bin/filter_out_ci, lib/maps.py: simplify(): also remove distinguishing #... suffix from terms (e.g. UNUSED#institutionID), to support mapping multiple columns to the special terms OMIT, PRIVATE, UNUSED (VegCore.vegpath.org#Special-terms), without creating a collision in the staging table renaming. note that this change must not be made to bin/canon, because this would cause suffixed terms to be autorenamed to their *un*suffixed VegCore versions.

bin/my2pg*: keep MySQL indefinite dates as text strings instead of translating them (to the first of the month or year) to fit into a PostgreSQL timestamp. this allows the application to decide how to handle these values, which otherwise have no corresponding value in PostgreSQL. this requires changing the date/time related types to text instead of leaving them as-is, so that they can store the custom MySQL strings.

bin/my2pg: use util.sh $top_dir instead of setting $selfDir

bin/my2pg*: use the util.sh sed wrapper, which fixes the LANG=*.UTF-8 "illegal byte sequence" errors on invalid UTF-8

bin/map: removed no longer used support for map.csv input column prefixes (expand out the prefixes instead). this used to be used by SpeciesLink to use just one mapping for a single term with multiple DwC namespaces, but was replaced with an explicit, ordered rather than implicit, unordered /_alt-ing together of the terms.

bin/map: removed no longer accurate comment that this is case- and punctuation-insensitive, since the case- and punctuation-insensitivity is now instead handled by map.csv preprocessing scripts before the mappings are even provided to bin/map

bugfix: bin/map: in_is_db: inline metadata value columns (used by new-style import) so that they can be compared by value in XML simplifying functions (lib/xml_func.py)

bin/map: map_table(): Resolve prefixes: combined db_xml.ColRef() constructor call with creation of args (as tuple) for clarity

bin/map: update_in_label(): use in_schema instead of the map spreadsheet column name when available, to allow using one spreadsheet for all datasources (which would not have a datasource-specific spreadsheet column name)

bin/src_map: support custom (or no) new_term_prefix. no new_term_prefix is useful for views whose columns have already been renamed in the underlying tables and should not have * re-prepended.

bin/make: moved $make_filter_active test to lib/sh/make.sh make() so that it's also used when make() is run directly (e.g. in a runscript) rather than via the bin/make wrapper in the PATH

bugfix: bin/make: use separate $make_filter_active flag instead of $is_outermost for avoiding duplicate output filtering, so that an outer runscript, which sets $is_outermost but does not activate the make filter, will not prevent the make filter from being activated when make is invoked

bugfix: bin/make: need to use sys_cmd instead of command so that the system make command is invoked instead of the wrapper (which would cause infinite mutual recursion for the ~/bien working copy, although not for the ~/Dropbox/svn working copy because nonrecursive=1 was able to remove the single recursion)

bin/make: use .rel to do relative includes

bugfix: bin/make: do not alter the PATH passed to the invoked make command, since this is a general-purpose wrapper and is not linked to a specific working copy (it could be used to wrap any make invocation, not just for commands in the svn dir). this uses lib/sh/local.sh's new PATH_add= flag.

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.

added bin/.rsync_ignore with filters from /README.TXT > Maintenance > to synchronize vegbiendev, jupiter, and your local machine. these filters will now be used with bin/sync_upload in addition to the periodic backup commands.

bin/tnrs_db: documented total runtime (10 days)

bin/tnrs_db: documented current runtime (162 ms/name)

bin/make_analytical_db: use new mk_table() instead of TRUNCATE/INSERT

bin/make_analytical_db: added mk_table() and use it in mk_analytical_table()

bin/make_analytical_db: added `/run export_` to make the geoscrub_input CSV export