README.TXT: put commands: removed unnecessary /** after dirs to exclude

README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: added steps to also backup the settings to Dropbox (in addition to jupiter)

lib/util.sh: added realpath () and use it where `readlink -f` is used

lib/util.run: doc comment: changed "run scripts" to "runscripts"

lib/util.run: factored general utils (non-runscript-specific) out into new util.sh

lib/util.run: renamed $verbose to $verbosity because it's an integer level, not a boolean. continue to support specifying the verbosity in $verbose.

lib/util.run: support $verbose="", which is treated as 0

lib/util.run: only automatically echo env vars when they are set if verbosity is >= 2

lib/util.run: added $verbose var to control logging. this is normally set to 0, but defaults to 2 for a runscript.

lib/util.run: moved `shopt -s expand_aliases` inside the include guard so callers can override the setting without it being reset if util.run is included again

lib/local.run: add $bin_dir to the PATH

bin/in_place: don't run if no command to run, because that would erase the file

bin/in_place: use -e (exit on error) option to sh instead of adding `|| exit` after every command

*run: added include guards

bugfix: lib/util.run: added include guard to prevent issues in "diamond includes", where a runscript includes two runscripts and each includes util.run, causing the second include of util.run to reset any methods overridden in the first included runscript. this prevents util.run from being included twice in the first place.

lib/util.run: added include_guard_var (), self_not_included () for use by path-based include guards

lib/util.run: echo_stdin (): print a separator before and after the echoed output to help distinguish it from other verbose output

lib/table.run: use new local.run instead of defining $bin_dir, etc. itself

lib/util.run: echo_export (): run the export builtin using `builtin` to avoid recursively calling any export alias or function defined by the user (e.g. `alias export=echo_export`. this causes util.run to be idempotent, such that it can be included multiple times without causing problems due to the redefinition of functions, vars, etc.

added lib/local.run, which links to locally-available resources such as $bin_dir

lib/table.run: added mysql (), mysql_ANSI ()

added web/links/index.htm containing Firefox bookmarks exported to HTML. CSS style information has been added to fix default HTML tag formatting, improve readability, and handle the Firefox bookmarks format. <dd> tags have been manually closed where HTML would not auto-close them properly. note that these changes must be reapplied each time the bookmarks file is reexported (`svn di` will show the changes to make).

lib/table.run: run mk_esc_name for $schema, $table

lib/table.run: added esc_name (), mk_esc_name ()

lib/util.run: added set_var ()

bugfix: lib/util.run: run_args_cmd (): `set --`: need to use eval so that the output of reverse is interpreted as escaped args rather than split using $IFS

bugfix: lib/util.run: run_args_cmd (): BASH_ARGV is stored in reverse order, so it needs to be reversed to be usable as $@

lib/util.run: added reverse ()

schemas/VegCore/VegCore.ERD.mwb: regenerated exports

schemas/VegCore/VegCore.ERD.mwb: source: renamed contact -> owner because smaller sources may not have an admin/contact person, but would have a copyright holder or other entity with control over the source's distribution

schemas/VegCore/VegCore.ERD.mwb: added table comments from VegCore data dictionary (VegCore.vegpath.org)

schemas/VegCore/VegCore.ERD.mwb: fixed lines

schemas/VegCore/VegCore.ERD.mwb: added hstore expansion columns where needed

schemas/VegCore/VegCore.ERD.mwb: fixed lines

schemas/VegCore/VegCore.ERD.mwb: specimen: added unique constraint for each set of identifying columns

schemas/VegCore/VegCore.ERD.mwb: collection: added back primary key

schemas/VegCore/VegCore.ERD.mwb: specimen: made owner an fkey to collection instead of organization to correspond with orig_collection and current_collection (and to allow auto-filling it from current_collection in a trigger)

schemas/VegCore/VegCore.ERD.mwb: specimen: reordered columns to group together each method of identifying a specimen

schemas/VegCore/VegCore.ERD.mwb: collection: don't inherit from source, because a collection is a scoping entity, not a dataset. a collection may also be used as a dataset, but need not be for the purposes of scoping a specimen's accession_number.

schemas/VegCore/VegCore.ERD.mwb: specimen: removed redundant stamping_institution and donor_institution, because these are now in orig_collection.institution. (it is assumed that stamping_institution and donor_institution are the same, because the first institution to acquire and store a specimen (the donor) is the one that stamps it with an accession_number.)

schemas/VegCore/VegCore.ERD.mwb: specimen: split collection into orig,current_collection because the collection that scoped the accession_number (the orig_collection) is sometimes different than the collection where the specimen is now held (the current_collection, or specimen_holder_institutions), e.g. when the specimen is donated

schemas/VegCore/VegCore.ERD.mwb: collection: added institution, name to identify and scope the collection

schemas/VegCore/VegCore.ERD.mwb: changed taxon_name fkeys to taxon_concept where appropriate, and renamed the referencing columns to *_taxon_concept to clearly indicate the referenced table. taxon_concept fkeys are appropriate whenever a taxon is defined or associated with an observed entity, in which case the assertion is not just to a taxon name but to a defined taxon concept (albeit sometimes an unofficial taxon concept scoped by the collector or identifier).

schemas/VegCore/VegCore.ERD.mwb: specimen: added code_in_individual column

schemas/VegCore/VegCore.ERD.mwb: specimen: added fkey to individual for the individual the specimen was taken from

schemas/VegCore/VegCore.ERD.mwb: individual/stem_observation: made individual/stem nullable because there is not always enough identifying information (stem tag, etc.) to actually associate an identifiable individual with an observation

schemas/VegCore/VegCore.ERD.mwb: moved code from individual to individual_observation because the code is something applied at observation time, rather than something that can be used to track individuals between observations

schemas/VegCore/VegCore.ERD.mwb: moved collection_event from taxon_occurrence to specimen because only specimens are actually collected, while other taxon_occurrences (e.g. individuals) must be uniquely identified by some means that are shared between re-observations (e.g. the stem tag)

schemas/VegCore/VegCore.ERD.mwb: moved collector, collector_number from taxon_occurrence to taxon_observation because these are actually attributes that are available or assigned at observation time, rather than being intrinsic to the taxon_occurrence (which can be either an individual or a specimen)

schemas/VegCore/VegCore.ERD.mwb: method: colored it forest green like stratum because these are both tables in the same category (method), and forest green is the color VegBank uses for methods. (the fact that VegBank gives stratum the method color indicates that we are on the right track when we are treating stratum as a type of method that's essentially a height class.)

schemas/VegCore/VegCore.ERD.mwb: method: added parent fkey which can be used to autoinherit attributes from another method, in the same way that event autoinherits a method from its parent

schemas/VegCore/VegCore.ERD.mwb: replaced < event label for diagram half with < place, because the occurrence half actually also includes events (observations), but does not include places

schemas/VegCore/VegCore.ERD.mwb: removed extra empty page used for moving objects around

schemas/VegCore/VegCore.ERD.mwb: swapped position of place and source categories so that the place tables, which users are apt to query often, are at the top, and the attribution information, which is likely to be used less often, is at the bottom. this also moves the plot table closer to taxon_occurrence, which should eventually have an fkey to it.

schemas/VegCore/VegCore.ERD.mwb: fixed lines

schemas/VegCore/VegCore.ERD.mwb: record: added source_id_scope and added it to the record_unique unique index

schemas/VegCore/VegCore.ERD.mwb: Default*ColumnType: updated to VARBINARY type used in key columns

schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps: repositioned arrow labels so they point in the direction of the fkey lines

schemas/VegCore/VegCore.ERD.mwb.run: use new zip/unzip_newer

lib/util.run: added zip/unzip_newer aliases

lib/util.run: added zip/unzip echo_run aliases

schemas/VegCore/VegCore.ERD.mwb.run: export_ (): always overwrite existing files. this option is safe, because -u only extracts files with a newer mtime than their copies on disk.

schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps labels: converted tables to notes, which now have bold formatting so that empty tables aren't needed for formatting purposes

schemas/VegCore/VegCore.ERD.mwb.run: import/export_ (): use zip/unzip's -u flag instead of `make` to auto-sync the zip file contents. the -u flag has the added benefit of preserving the contained file's mtime, at the expense of an mtime lookup in the zip archive's table of contents.

added schemas/VegCore/VegCore.ERD.mwb.run, which syncs VegCore.ERD.mwb's zip file contents

bugfix: lib/util.run: inline_make (): put echo_func at the top of the function

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: inline_make (): use <() to pass Makefile commands as a named descriptor rather than using stdin, to allow stdin to be used by commands that prompt the user

bugfix: lib/util.run: echo_vars (): remove any value to set (=*) from the vars, since this is often used with export

bugfix: lib/util.run: echo_export (): set the vars before echoing them

lib/util.run: run_args_cmd (): use new canon_rel_path() to resolve .. in the script path, so it's easier to see where the script is actually located

lib/util.run: echo_func (): use new canon_rel_path() to resolve .. in the script path, so it's easier to see where the script is actually located

lib/util.run: added canon_rel_path ()

lib/util.run: inline_make (): provide $self as make var

lib/util.run: inline_make (): provide self_dir to make as env var instead of as make var, to avoid specifying every make var both as a local var and as a make var in the make command

lib/util.run: export alias: added comment explaining what it does

lib/util.run: aliased export to echo_export so all env vars are automatically echoed when they are set

lib/util.run: added echo_vars (), echo_export ()

lib/util.run: inline_make (): added local $self and use it to create $self_dir

lib/util.run: inline_make (): set $self_dir as a local var before passing it to make, to avoid clutter in the command that invokes make

added schemas/VegCore/document.mwb.xml, so changes to the diagram can be tracked line-by-line. keeping this up-to-date requires running `unzip VegCore.ERD.mwb document.mwb.xml` whenever VegCore.ERD.mwb is changed.

schemas/VegCore/VegCore.ERD.mwb: target MySQL version: updated to 5.5.3

schemas/VegCore/VegCore.ERD.mwb: NoteFigure:TextFont (labels): made it bold to stand out better

schemas/VegCore/VegCore.ERD.mwb: Layer:TitleFont (legends): increased size and made it bold to stand out better

schemas/VegCore/VegCore.ERD.mwb: made stratum extend method, so that any observation event can have an associated stratum. removed no longer needed plot_stratum, since strata are now represented as sampling methods (i.e. using height classes) rather than a variant of subplots.

schemas/VegCore/VegCore.ERD.mwb: VegCore DB: changed collation to utf8_bin to match table collation

schemas/VegCore/VegCore.ERD.mwb: saved settings for publishing schema to vegbiendev phpMyAdmin (vegbiendev.nceas.ucsb.edu/phpmyadmin/index.php?db=VegCore). this adds `DROP TABLE IF EXISTS` before each CREATE TABLE statement, renames the default DB to VegCore, and adds a USE statement to select the VegCore DB.

schemas/VegCore/connections.xml: vegbiendev.nceas.ucsb.edu: set schema (DB) to VegCore

added schemas/VegCore/connections.xml, which should be installed as the connections.xml settings file

schemas/VegCore/VegCore.ERD.mwb: imported database connections from the connections.xml settings file into document.mwb.xml in the .mwb zip file. these connections are not used directly by MySQL Workbench, but instead need to be copied into the connections.xml settings file.

schemas/VegCore/VegCore.ERD.mwb: use Database > Forward Engineer (Ctrl+G) instead of File > Export > Forward Engineer SQL CREATE Script (Ctrl+Shift+G), so that comments will use the max comment length for the server's MySQL version rather than MySQL Workbench's internal MySQL version, which has a max comment length of only 60 chars for tables. this commit stores the default export settings for Forward Engineer, which are saved each time it's run.

bugfix: root Makefile: $(postgresReload-Linux): fixed the "shmat(id=...) failed: Cannot allocate memory" error by telling the user to restart PostgreSQL manually from the command line

root Makefile: $(postgresReload-Linux): don't restart Postgres twice, because this does not fix the "shmat(id=...) failed: Cannot allocate memory" error. this error is instead produced whenever PostgreSQL is restarted from within a Makefile, but not when it's run directly from the command line or /bin/sh.

root Makefile: $(postgresReload-Linux): restart Postgres twice, because the first time after the postgresql.conf has been udpated, it always produces a "shmat(id=...) failed: Cannot allocate memory" error

schemas/VegCore/VegCore.ERD.mwb: re-synced with VegCore.my.sql: step 2: `DEFAULT NULL` added on all nullable columns

schemas/VegCore/VegCore.ERD.mwb: re-synced with VegCore.my.sql: step 1: table order changed

schemas/VegCore/VegCore.ERD.mwb: relationship: renamed the two fk_relationship_record1 fkeys so their names wouldn't collide

schemas/VegCore/VegCore.ERD.mwb: changed encoding back to utf8/utf8_bin now that latin1 isn't needed to make the key columns satisfy the index length limits. note that the connection encoding must be utf8 on import so that the correct byte sequence is stored in the VARBINARY columns.

schemas/VegCore/VegCore.ERD.mwb: changed VARCHAR BINARY columns to VARBINARY because VARCHAR BINARY is actually only an alias for the *_bin collation of the table's encoding, but still uses multibyte characters if the encoding does. note that VARBINARY will still be displayed as text (in the connection encoding), rather than hex values.

schemas/VegCore/VegCore.ERD.mwb: changed the type of TEXT columns used in indexes to VARCHAR BINARY to satisfy prefix length limits ("a prefix can be up to [...] 767 bytes for InnoDB tables" <http://dev.mysql.com/doc/refman/5.5/en/create-index.html&gt;). the BINARY flag was added to allow storing Unicode values (from UTF-8), which are not representable in the latin1 encoding.