bugfix: /Makefile: bin/install: also need to install uutils

*{.sh,run}: use standard WARNING syntax for warning labels

fix: lib/sh/util.sh: verbosity_compat(): documented that this should not be run until right before executing an external command, so that it doesn't mess up the logging mechanism

bugfix: bin/make: don't run verbosity_compat until right before executing the external command, so that it doesn't mess up the logging mechanism. this is run automatically by command(), so there is no need to do anything here. note that logging bugs like these can now be troubleshooted much more easily with pst() to narrow down which functions could be causing the problem.

bugfix: lib/sh/util.sh: functions called by pst(): commented out/removed logging calls that would have caused infinite recursion when pst()'ing a logging function

lib/sh/util.sh: echo_func(): get call context before wrapper(s), which is more useful for debugging. this uses skip_stack_frames()'s lookahead=1 mode.

fix: lib/sh/util.sh: skip_stack_frames() callers: updated for new skip_stack_frames rather than get_stack_frame behavior

lib/sh/util.sh: skip_stack_frames(): added lookahead support, which looks at entry after current to deterine whether to skip current. this is useful for skipping wrappers, by looking at the calling function's name.

fix: lib/sh/util.sh: skip_stack_frames(): for new skip_stack_frames rather than get_stack_frame behavior, stack frames must be skipped in the caller to preserve the stack frame pointer

lib/sh/util.sh: get_stack_frame_after(): renamed to skip_stack_frames() for clarity

lib/sh/util.sh: added skip_stack_frame_in_caller, unskip_stack_frame_in_caller

lib/sh/util.sh: added prev_stack_frame

lib/sh/util.sh: echo_func(): use new format_stack_frame, which adds call context information to what was provided by func_loc

fix: lib/sh/util.sh: format_stack_frame(): need to hide canon_rel_path() info using log+

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

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

lib/sh/util.sh: next_stack_frame: documented usage

fix: lib/runscripts/util.run: runscript template: all(): moved example commands to target(), where they would more likely be located

lib/sh/util.sh: format_stack_frame(): support including args

lib/sh/util.sh: debugging: added pst() (print_stack_trace)

lib/sh/util.sh: added stack_trace(), print_stack_trace()

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

lib/sh/util.sh: added get_stack_frame() and helpers

lib/sh/util.sh: terminal: moved before errors so it can be used by it

lib/sh/util.sh: errors, debugging: moved after datatype sections so their functions can use these

bugfix: lib/sh/util.sh: canon_rel_path() stub: proper no-op requires passing through original path

lib/sh/util.sh: canon_rel_path(): fall back to original path if can't resolve, instead of errexiting

bugfix: lib/sh/util.sh: canon_rel_path(): don't re-localize $path because this clears it

lib/sh/util.sh: canon_rel_path(): import $1 to $path before function body, so that the function body can be moved to a nested function

lib/sh/util.sh: added canon_rel_path() stub for use by debugging functions

bugfix: /Makefile: install: run bin/install first since config/download depends on it

lib/sh/util.sh: moved func_loc() to before debugging section so it can be used by debugging functions

bugfix: lib/sh/util.sh: command__exec(): need to restore $verbosity before calling die_e

bugfix: /Makefile: install: also need to run config/download to get the necessary passwords

config/Makefile: added download target

/Makefile: config: renamed to bin/install because config is the name of a directory

/README.TXT: Installation: `make install`: added instructions for what to do at each prompt

/README.TXT: Installation: Check out svn: need to install svn first as this does not come preinstalled on Ubuntu

fix: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: make(): added warning that this will truncate the geoscrub database tables

/README.TXT: to back up the local machine's hard drive: just do a single pass, to avoid the numerous different steps

backups/*retention_policy*: on jupiter: changed to avoid retaining backups further back, as these consume significant disk space on jupiter and are not useful for anything

fix: lib/sh/local.sh: $sync_remote_url: need $USER so user can be overridden when running as root

fix: /README.TXT: to back up the local machine's settings: to jupiter: need `sudo -E` for new Documents/BIEN/vegbiendev*/

/README.TXT: backups of ~/.dropbox/: just pause and resume Dropbox instead of quitting and restarting it

/README.TXT: to back up the local machine's settings: to Dropbox: exclude gmvault-db/ to save space in Dropbox

/README.TXT: to back up the local machine's settings: don't need to exclude ~/Library/Thunderbird/Profiles/9oo8rcyn.default/global-messages-db.sqlite because the disk that was corrupting this file has been replaced (#907)

/README.TXT: to back up e-mails: don't need to also sync aaronmk@nceas.ucsb.edu because these e-mails are also in aaronmk.nceas@gmail.com (auto-forwarded)

/README.TXT: Notes on system stability: removed no longer applicable warning about system upgrades, which is now incorrect because the disk space overrun bug (#887) was found not to have been caused by a system upgrade

web/links/index.htm: updated to Firefox bookmarks: Roundtable: added links for Roundtable on "obstacles faced by researchers who reuse, share and manage data, and strategies for overcoming them"

lib/Firefox_bookmarks.reformat.csv: label page's self-description as such: also support quotations enclosed in '

fix: exports/native_status_resolver.csv.run: added `users_by_name=1` to preserve the file group

added inputs/VegBank/run.call_graph.log

inputs/VegBank/run.log: updated for echo_vars() changes. the PG* vars, which contain important information, will now not need to be filtered out.

lib/sh/util.sh: echo_vars(): merge repeated flags so there aren't flags in between the vars (which is also not valid declare syntax)

lib/sh/db.sh: pg_cmd(): log vars on same line to avoid clutter

lib/sh/util.sh: echo_vars(): put all the vars on the same line so they don't clutter up the call graph generated at the default verbosity

web/links/index.htm: updated to Firefox bookmarks: Mac: added link for VNC client. extended attributes: added link for chflags.

added planning/workflow/staging_tables_installation_for_SQL_datasource.odg.src.log

added inputs/VegBank/run.log

fix: inputs/input.Makefile: $(svnFilesGlob): *.log should be in both the subdirs and the main dir

inputs/input.Makefile: $(svnFilesGlob): *.log

inputs/Makefile: install: install an empty VegBIEN schema instead of all the datasources, at Mark's request. this enables loading just a single datasource.

schemas/VegBIEN/data_dictionary/VegBIEN data dictionary.xlsx: updated

bugfix: schemas/public_.sql: view_full_occurrence_individual_view and related views: synced to data dictionary spreadsheet, which adds back the links to the definitions (which used to be part of the column name itself)

fix: schemas/public_.sql: analytical_plot, analytical_specimen: updated column names to be the same as analytical_stem, which these are a subset of

/README.TXT: to synchronize vegbiendev, jupiter, and your local machine: avoid extraneous diffs when rsyncing: clarified the machines that the command should be run on

web/links/index.htm: updated to Firefox bookmarks: removed broken favicons

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

fix: /README.TXT: to backup files not in Time Machine: need to use 2 TB external hard drive instead of Time Machine drive because Time Machine drive does not have ~/Documents/BIEN/ in a location where it can be hardlinked against

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

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

web/links/index.htm: updated to Firefox bookmarks: local machine phpPgAdmin: removed this so the Mac won't get woken up on network access whenever someone opens the links page, which attempts to load the favicon from the local machine. the previous solution of manually deleting the favicon (r13406) doesn't work because the favicon will just get re-added whenever this bookmark is visited.

web/links/index.htm: updated to Firefox bookmarks: find: added instructions for searching by <>, not just =

/README.TXT: Datasource setup: For MS Access databases: added that one should use the settings in the associated .ini file where available

/README.TXT: Datasource setup: For MS Access databases: program link: added page subsections

/README.TXT: to backup files not in Time Machine: note that Time Machine dereferences hard links: added commands documenting that this is the case

fix: /README.TXT: to backup files not in Time Machine: on first run, create parent dirs: added mkdir for Postgres

bugfix: /README.TXT: to backup files not in Time Machine: on first run, create parent dirs: mkdir: need sudo

/README.TXT: to backup files not in Time Machine: moved to root/ subdir to group the multiple top-level dirs together

/README.TXT: to backup files not in Time Machine: added the vegbiendev archival backups, which cannot be backed up by Time Machine because it dereferences hard links

/README.TXT: to backup files not in Time Machine: documented why Postgres cannot be backed up by Time Machine

/README.TXT: Single datasource refresh: added steps to place the updated extract and extracted flat file(s)

/README.TXT: Single datasource refresh: connect to vegbiendev first, even though steps before it have their own step to do this

/README.TXT: Single datasource refresh: reimport_scrub: added step to view progress

/README.TXT: Single datasource refresh: moved to top since these steps are performed more often

added planning/workflow/BIEN data workflow-2_bje.png export

planning/meetings/BIEN conference call availability.xlsx: updated

planning/workflow/BIEN data workflow-2_bje.pptx: updated with Martha's changes and changes during conference call

bugfix: web/BIEN3/Redmine/.htaccess: subpath redirect: also redirect dirs, so that empty-subdir main-page redirects (eg. wiki.vegpath.org) work properly

bugfix: web/BIEN3/Redmine/.htaccess: main page should continue to redirect to wiki, not Redmine project page

schemas/public_.sql: *_view: re-ran *_view_modify(), which use the new non-blocking rematerialize_view()

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: view_full_occurrence_individual: re-ran view_full_occurrence_individual_view_modify(), which uses the new non-blocking rematerialize_view()

schemas/util.sql: rematerialize_view(): made it non-blocking, so that it would allow full access to the original materialized table during the operation

schemas/util.sql: added identifier_replace()

schemas/util.sql: added relation_replace()

/README.TXT: Single datasource import: renamed to Single datasource refresh since it works on existing datasources

/README.TXT: Single datasource import: also need to reload staging tables

/README.TXT: Single datasource import: added steps to re-run geoscrubbing and back up the vegbiendev database

planning/workflow/BIEN data workflow-2_bje.pptx: fixed text alignment