/.htaccess: use canonical URL without symlinks

added /.htaccess to create the right self-referential URL since / is outside the document root (linked from /vegbiendev/fs/)

schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps: moved labels to the start of the arrow they label, so that the user can more easily follow the arrows from step to step by looking for an outward-pointing arrow with a label

added inputs/GBIF/_MySQL/MySQL.data.sql.gz.md5

bugfix: lib/common.Makefile: Compression: %.gz <-> %: only run command if target does not exist, to avoid overwriting the target when the compressed or uncompressed version is newer than it. the difference in mtimes can arise when one file is created after the other, and should not cause the opposite operation to be performed to try to make the other file up-to-date (leading to an infinite back-and-forth of creating one file from the other).

web/links/index.htm: updated to Firefox bookmarks. the VegPath link now includes the new favicon.

added web/favicon.ico generated from schemas/BIEN_logo.png

web/main.conf: added SSL-protected site for use with password-protected areas of the site, so that the user's password is not transmitted in plaintext. (because the SSL certificate is self-signed, it will unfortunately display the Confirm Security Exception message in Firefox.) note that digest authentication cannot be used to avoid plaintext passwords, because it requires knowing the user's original password to generate the digest, but we have only the MD5 sums in /etc/shadow.

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

web/links/index.htm: put all bookmarks into one subfolder named BIEN links, to facilitate importing them all into one folder on another machine. this also helps when upgrading to a newer version of the bookmarks, because the previous version must be deleted and this now requires deleting only a single folder.

lib/Firefox_bookmarks.reformat.csv: use <H3 style="font-size: 200%;"> instead of <H1> to make the first folder's name the page title, so that Firefox can reimport the first folder as a bookmarks folder

bugfix: lib/Firefox_bookmarks.reformat.csv: make first folder name the page title: added back replacement string

web/links/index.htm.run: clean_up (): removed command to add page title because this is now done by lib/Firefox_bookmarks.reformat.csv

lib/Firefox_bookmarks.reformat.csv: use page title as window title

lib/Firefox_bookmarks.reformat.csv: remove previous page title

lib/Firefox_bookmarks.reformat.csv: make first folder name the page title

lib/Firefox_bookmarks.reformat.csv: move Bookmarks Toolbar inside first folder instead of before it. this allows storing all bookmarks in one subfolder so that when the web page is imported into another computer's bookmarks, the imported bookmarks are all together in one folder.

bugfix: lib/Firefox_bookmarks.reformat.csv: refactored regexps to account for Python applying (?s) to the entire regexp, even if it appears inside a () subgroup. the Python behavior is in contrast to the standard regexp behavior used by Java, etc. where (?s) applies only to the subgroup it appears in.

web/links/index.htm: updated to Firefox bookmarks. resources: put unsorted links into subfolders.

bugfix: lib/Firefox_bookmarks.reformat.csv: add <style>: format bookmark description as plaintext: use `white-space: pre-wrap` instead of pre in order to wrap long lines

bugfix: lib/Firefox_bookmarks.reformat.csv: favicon images: made replacements idempotent so that the favicons would not be deleted the next time the web/links/index.htm.run is run (due to a newline being added before ICON= )

lib/Firefox_bookmarks.reformat.csv: favicon images: display placeholder favicon image for every link to ensure uniform alignment

added web/links/blank.gif symlink to web/blank.gif for shorter blank.gif URLs

added web/blank.gif

lib/Firefox_bookmarks.reformat.csv: display ICON attributes as separate images. note that this uses the "data:" embedded image contents provided in the bookmarks file, so the images load instantly along with the page instead of needing to be separately retrieved from each server.

lib/Firefox_bookmarks.reformat.csv: instead of removing ICON attributes with favicon contents, put them on their own line so the rest of the line is easier to see

lib/Firefox_bookmarks.reformat.csv: divided replacements into sections

lib/Firefox_bookmarks.reformat.csv: move Bookmarks Toolbar to beginning, remove its desc, and rename it to Quick links

web/links/index.htm: removed extra divider after Recent Tags, Recently Bookmarked because section dividers interfere with regexp matching and the Bookmarks Toolbar is already visually separate from them

web/links/index.htm: moved Recent Tags, Recently Bookmarked special folders to end because they are Firefox-specific and not part of the BIEN links (they also do not work in a browser because they are Firefox-specific query bookmarks instead of actual folders)

web/links/index.htm.run: clean_up (): rename the page title from "Bookmarks" to "BIEN links"

bin/repl: skip header instead of parsing it, since its columns are not used. this also allows using just a blank line as the header when the column names are not important.

web/links/index.htm: use initial blank line instead of previous "-" workaround to indicate author comment at start of bookmark desc

web/links/index.htm: use initial blank line to indicate author comment at start of bookmark desc

lib/Firefox_bookmarks.reformat.csv: label page's description: don't label a bookmark desc starting with a blank line (indicating an author-added comment) as a page's description

lib/Firefox_bookmarks.reformat.csv: label page's description: don't label an author-added quotation (which starts with " ) as the page's description

bin/in_place: set the permissions of the new file to the original file when `chmod --reference` is available. this ensures that when a file is marked web-accessible, it stays web-accessible when you run an in_place command on it.

web/links/index.htm: BitTorrent Sync: security warning about data leak: added link to reported bug at http://forum.bittorrent.com/topic/18612-security-hole-in-linux-webui-makes-all-your-files-publicly-accessible/ . updated workaround instructions.

web/links/index.htm: updated to Firefox bookmarks. BitTorrent Sync: added security warning that running btsync on Linux will by default create a publicly-accessible, unprotected WebUI, allowing anyone on the web to create a sync folder to view and edit any of your files. to avoid this, always run btsync with a config file which sets a password on the WebUI. if you have already run btsync, run `killall btsync` to turn off the WebUI.

web/links/index.htm: updated to Firefox bookmarks. changes include links about BitTorrent Sync.

lib/Firefox_bookmarks.reformat.csv: label <meta> description: renamed label text to "page's description" to be understandable to non-programmers

lib/Firefox_bookmarks.reformat.csv: label <meta> description: remove any existing description label, to avoid duplicating the description label when the text of the description label changes

lib/Firefox_bookmarks.reformat.csv: label <meta> description as such to avoid confusing it with comments added by the bookmark author, who may not agree with it. the <meta> description is in the 1st paragraph(s), when provided.

lib/Firefox_bookmarks.reformat.csv: remove LAST_MODIFIED attributes, which seem to change whenever the favicon is updated and clutter up the svn diff

lib/Firefox_bookmarks.reformat.csv: remove ICON attributes with favicon contents, which clutter up the svn diffs

added web/links/index.htm.run with clean_up action to run whenever the index.htm bookmarks file is changed (`web/links/index.htm.run clean_up`)

added lib/Firefox_bookmarks.reformat.csv

README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: exclude only backup files in the Documents/BIEN/svn/backups/ dir (sync the other files)

README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: when changes are made on vegbiendev: don't sync the group, which can be bien on vegbiendev but not on jupiter (where aaronmk is not a member of the bien group)

README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: when changes are made on vegbiendev: include *.md5

README.TXT: Maintenance: removed step to backup the Ubuntu VM, because this is now done as part of the "backup files not in Time Machine" step

README.TXT: Maintenance: added steps to backup files not in Time Machine

README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: back up (almost) all files in the home directory instead of just Library/ (to both jupiter and Dropbox)

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