/Makefile: phppgadmin-Linux: removed no longer needed $(editApacheConfForPhppgadmin), as phpPgAdmin no longer uses this file (/etc/phppgadmin/apache.conf)
/Makefile: phppgadmin-Linux: removed no longer needed $(editPhppgadminApacheConf)
/Makefile: misc-Linux: added htop
/Makefile: misc-Linux: added jedit
/Makefile: postgres-Linux: added pgadmin3
bugfix: /Makefile: $(postgresReload-*) calls: do not prepend $(MAKE) or - because these are multi-command functions
bugfix: /Makefile: $(bien*Password): need to use = instead of := because these files are not available until config/download/live has run
fix: /README.TXT: Installation: added instructions for "aaronmk@jupiter's password" prompt
/README.TXT: Installation: added step to open a terminal window
fix: /README.TXT: Installation: added instructions for "Are you sure you want to continue connecting" prompt
inputs/VegBank/run*.log: updated. this adds the function call context in addition to the function location.
bugfix: /Makefile: $(uutils_install): need to exit after printing instructions instead of continuing
fix: /README.TXT: Installation: need instructions for "reload PATH" prompt
fix: /README.TXT: Installation: `apt-get install subversion`: need --yes
bugfix: /Makefile: bin/install: uutils: need to reopen terminal window before can proceed with other installation steps
/Makefile: python-Linux: removed no longer used installation of pp (Parallel Python). we use Python's multiprocessing package instead.
bugfix: /Makefile: install: must be config/download/live, not config/download
README.TXT: bin/sync_upload calls as root: don't need to set $USER because this is now set to the correct value in bin/sync_upload's scripts
bugfix: lib/sh/local.sh: $sync_remote_url: jupiter user is always aaronmk, not the local user
*{.sh,run}: use standard WARNING syntax for warning labels
bugfix: /Makefile: bin/install: also need to install uutils
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: 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