lib/util.run: run_cmd (): renamed to run_args_cmd to clarify that this runs only the command line args command, not any command. added doc comment to clarify this.

lib/util.run: EXIT trap: use on_exit() function which calls run_cmd instead of having run_cmd be the handler, so that users can override this function to perform other commands (or no commands) after the script is read

lib/util.run: echo_func (): use the caller's FUNCNAME via the $FUNCNAME[] array instead of requiring them to pass it in the function args as `echo_func "$FUNCNAME" "$@"`

README.TXT: Maintenance: added steps to synchronize a Mac's settings with my testing machine's

README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: moved swap=1 right before src= dest=, which it applies to. aligned whitespace of the various commands.

README.TXT: Maintenance: steps to synchronize vegbiendev, jupiter, and your local machine: added steps to install dependencies

README.TXT: Maintenance: Added steps to synchronize vegbiendev, jupiter, and your local machine when changes are made on vegbiendev

README.TXT: converted spaces to tabs for easier readability in a whitespace-highlighting text editor, and so that pressing backspace deletes an indent rather than just a character (creating a misaligned indent)

Moved validation/ under planning/workflow/

Moved planning/use_cases/ under planning/goals/

Moved planning/milestones/ under planning/timeline/

Added inputs/VegBIEN/planning shortcut to fs/planning

web/.fs: symlink via datasources/VegBIEN/fs instead

Added inputs/VegBIEN/fs symlink to /servers/vegbiendev/fs

Added web/.gbif shortcut to datasources/GBIF

web/**/.htaccess: Use [qsappend] flag with all RewriteRules to ensure that the original query string is never lost

inputs/VegBank/.htaccess: Added RewriteCond to check that the REQUEST_FILENAME is not an existing dir, which is apparently needed to prevent the verify/ subdir from being interpreted as a redirect

web/**/.htaccess: Removed preprocessing commands that need to run for every dir, because these are now inherited from the outermost .htaccess using InheritBefore. This allows the inner .htaccess files to focus just on the fallback rewrites, without needing lots of boilerplate code (except for the obligatory RewriteEngine/RewriteOptions/SetEnvIf preamble).

web/.htaccess: handle DirectoryIndex subrequests when there is no DirectoryIndex, by deleting the /index filename. This ensures that any fallback redirect is not invoked, and instead the action corresponding to a trailing / (usually the display of a directory listing) is performed.

web/**/.htaccess: Use InheritBefore RewriteOption so that the outermost dir's rules are always run first. This is necessary so that all the HTTP_HOST and dotpath handlers, etc. are applied before any fallback handlers, without needing to copy and paste each rule into every .htaccess file. (Note that the InheritBefore RewriteOption is only available in Apache 2.4.) The outermost .htaccess file, however, must not use InheritBefore because this would inherit rules from the global Apache config, which normally should not be run and which cause an infinite redirect loop.

web/**/.htaccess: fallback rules which should not be inherited by subdirs: Filter using a RewriteCond on %{ENV:innermost_dir} so that the rule is only run if the innermost dir was this dir. (This is needed when using InheritBefore.)

web/**/.htaccess: Added SetEnvIf directives to set the $innermost_dir env var, which is used by InheritBefore RewriteRule inheritance. You can easily populate the current dir name in jEdit by right-clicking the buffer tab and selecting Insert File Path (which requires the BufferTabs plugin), and then picking out the dir right before the .htaccess. If multiple dirs in the dir path have the same name (e.g. a/b/a/), add a distinguishing prefix to the inner dirs (this is rare).

web/.htaccess: Support rules being inherited by subdirs using InheritBefore, by setting an env var $innermost_dir that stores the name of the innermost subdir to contain an .htaccess file. This env var can then be tested for in a RewriteCond in rules that should only apply locally. This works because SetEnvIf processes directives from the outer dir to the inner dir, so that the inner dir's setting comes last and is the final value of $innermost_dir. Note that you must use SetEnvIf rather than SetEnv because "The internal environment variables set by [SetEnv] are set after most early request processing directives are run, such as access control and URI-to-filename mapping. If the environment variable you're setting is meant as input into this early phase of processing such as the RewriteRule directive, you should instead set the environment variable with SetEnvIf." [emphasis added] (http://httpd.apache.org/docs/current/mod/mod_setenvif.html#setenvif)

web/.htaccess: don't rewrite existing paths: Changed match string to what is used in subdirs, so that if this rule is inherited, what is considered an existing path (i.e. a file or subdir) is restricted appropriately

web/**/.htaccess: no-replacement RewriteRules: Removed the standard [discardpath,noescape] flags because they add unnecessary clutter and are not needed for this type of rule. Note that these flags are still required on regular RewriteRules which have a replacement string.

web/**/.htaccess: no-replacement RewriteRules: Use just ^ as the match string because there is no need to actually match characters. This also makes it easy to visually tell what is a no-replacement RewriteRule vs. a RewriteRule that matches the entire path.

web/.htaccess: Renamed $REQUEST_URI_NO_SLASH to $REQUEST_URI_no_/ to take advantage of (some) special chars being allowed in env var names

Added web/people/

web/.htaccess: fallback redirect: Use new VegCore/ instead of specifying the full wiki URL

schemas/VegCore/.htaccess: Fixed bug where need to issue explicit redirect because path contains a fragment (#...), which must be sent to the browser

Added schemas/VegCore/.htaccess

Added web/.vegcore shortcut to exchange_schemas/VegCore

Added root .htaccess (accessed via web/servers/vegbiendev/fs or one of its shortcuts)

web/.htaccess: translate subdomain to path: Use new REQUEST_URI_NO_SLASH to avoid adding an automatic trailing / when a subdir was reached as a subdomain without a path (e.g. VegBank.vegpath.org), which should be equivalent to going to the subdir's homepage (vegpath.org/VegBank) rather than to its directory listing (vegpath.org/VegBank/ ; note the trailing /)

web/.htaccess: set REQUEST_URI_NO_SLASH for use by translating subdomain to path

Added web/.fs symlink to .vegbiendev/fs

web/svn-web, wiki: Made them hidden so they wouldn't appear in the dir listing (which should not contain shortcuts to inner paths, as these would create significant clutter). web/svn unfortunately can't be made hidden because there is already a .svn dir.

Added web/.nimoy, .vegbiendev shortcuts

web/DwC, VegX: Replaced with versions in exchange_schemas/

Moved web/TCS/ to schemas/

Added web/exchange_schemas/ symlink

Removed web/exchange_schemas/ in preparation for making it a symlink

Added schemas/.htaccess

Added web/exchange_schemas/

Merged web/DwC,VegX with the corresponding dir in schemas/

Moved web/BIEN2, IH into aggregators/

Moved web/BIEN2, IH into aggregators/

Added web/aggregators, primary_databases with symlinks to the applicable datasources

web/.tnrs: Updated to point to datasources/.TNRS/

Removed web/TNRS/ in preparation for replacing it with a symlink

Added inputs/.TNRS/.htaccess

web/.redmine/: Updated for new VegBIEN/ location

web/.htaccess: Use new %{REQUEST_SCHEME} to construct self-refential URLs

web/VegBIEN/: Moved to datasources/

Added inputs/.htaccess, which parses dotpaths and adds trailing / when datasources/ subdir is listed. (DirectorySlash cannot be used for this because it would affect all subdirs, too, which must not have DirectorySlash on. Turning DirectorySlash off in each subdir would not work, because the / is added as soon as a valid filesystem path is formed, even if the inner dir would not have added the /.)

web/**/.htaccess: internal redirects: Use ?&$0 instead of just ?$0 to prevent the query string from being reinterpreted as a dotpath by the destination dir

web/VegBIEN/Redmine/*/.htaccess: Use relative URL paths. This requires adding a RewriteBase directive because these dirs can be reached by symlinks.

inputs/SALVIAS/.htaccess: Removed test RedirectMatch directive

web/**/.htaccess: RewriteOptions: Redirect dir paths without the trailing / to the datasource's homepage, and let dir paths with the trailing / point to the directory index. This is the opposite of the way it was before, and is more intuitive because the trailing / indicates a directory listing, while the trailing / would generally be omitted when linking to the datasource itself.

web/**/.htaccess: handle DirectoryIndex subrequests, which append "index" to the dir

web/**/.htaccess: RewriteOptions: Removed inherit because if the destination is not found in the current dir, a 404 should be returned instead of trying to invoke the parent dir's fallback handler (which applies only to paths in the parent dir). Ideally, we would use InheritBefore to get the subdomain preprocessing, etc., but the parent dir's fallback handler would still need to be turned off somehow when the rule was being run by a subdir.

web/.htaccess: Only forward specific terms (subpaths) to VegCore, not also the dir index itself

web/**/.htaccess: RewriteOptions: Added AllowNoSlash (available in Apache 2.4) so dir paths without the trailing / can be parsed by mod_rewrite

web/.htaccess: Turned off DirectorySlash so that the dir without the trailing / can have a separate meaning (e.g. as the home page of a datasource, rather than a listing of the short URLs available for it)

web/main.conf: <Directory .>: Added `Require all granted`, which is needed by Apache 2.4 to prevent 403 Forbidden errors. This change breaks compatibility with older versions of Apache, but is unfortunately required by 2.4.

web/**/.htaccess: parse dotpath in the query string: Use just dotpath instead of dotpath.php because the extension is added automatically by MultiViews

web/**/.htaccess: parse dotpath in the query string: Remove any index.* suffix, which is added by MultiViews in Apache 2.4

web/main.conf: Updated the path of the <Directory> directive for the DocumentRoot

web/.htaccess: Set Options +Indexes because this isn't the default in Apache 2.4

web/.htaccess: DirectoryIndex: Use index instead of hardcoding index.php because MultiViews will now add the appropriate extension automatically

web/.htaccess: Turn on MultiViews to allow auto-adding of the file extension

inputs/**/.htaccess: Use a direct filesystem path rather than going through /svn (the Redmine web interface) because this loads much faster, and avoids needing to manually specify svn-web instead of svn for files that should be displayed in the browser instead of downloaded. It also adds support for files not in svn. Note that the use of a relative RewriteRule replacement requires RewriteBase when the directory is not under the document root, in order to construct the correct self-referential URL (http://httpd.apache.org/docs/current/mod/mod_rewrite.html#rewritebase).

inputs/**/.htaccess: Removed no longer needed trailing / in paths

inputs/CTFS/*/.htaccess: Use new direct shortcuts to /Redmine subtrees

Added wiki shortcut to Redmine/wiki

web/.htaccess: use separate lowercase version when available: Support paths without a trailing /

web/.htaccess: use separate lowercase version when available: Fixed bug where need to use [last] flag, in order to rewrite in the new subdir instead of applying the rest of this dir's rules (which would forward to VegCore)

web/: datasources indexed in VegPath: Link to the corresponding inputs/ dir instead, which now stores the data and the short URLs in one place

web/.htaccess: Use %{REQUEST_URI} ("The path component of the requested URI" <http://httpd.apache.org/docs/current/mod/mod_rewrite.html#rewritecond&gt;) instead of /$0, in order to preserve whether or not the path had a trailing slash. This also ensures that the rule functions correctly if it is invoked in a subdir context, which may occur for the "remove www subdomain" rule.

web/.htaccess: Removed "don't redirect subdir paths" because this is now handled by "don't rewrite existing paths" as described in r8375

web/: datasources indexed in VegPath: Added .htaccess files to corresponding inputs/ dir so the short URLs can also be accessed via VegBIEN's own dir for the datasource

inputs/input.Makefile: Removed .PRECIOUS from %/header.csv, %/map.csv so that these scripts are deleted on error. This is useful for the runscripts and for non-data dirs whose header.csv cannot be made.

inputs/input.Makefile: SVN: Only run %/add on subdirs with visible (non-hidden) files. Subdirs with only hidden files (e.g. .htaccess) are assumed to be non-data dirs.

inputs/input.Makefile: Staging tables installation: %/install: $(logInstall): Only use log file if log dir exists, to support non-data dirs

inputs/input.Makefile: Staging tables installation: %/install: ignore errors in $(exportHeader) and $(cleanup) if the table does not exist (i.e. a non-data dir)

inputs/input.Makefile: Staging tables installation: %/install: Don't run $(import_install_) for empty dirs because there is no data to import

lib/sql.py: parse_exception(): typed_name_re: Fixed bug where need to require the "" around the table/column name, because otherwise, the regexp will try to match as few characters as possible, causing it to match only the first letter of the name

web/**/.htaccess: Removed "handle DirectoryIndex" rule, which does not appear to be needed with the new dotpath format

web/VegBank/.htaccess: RewriteRule: Fixed bug where need to match tables by themselves as well as followed by columns

web/**/.htaccess: Added "don't rewrite existing paths" and "handle DirectoryIndex" rules to all .htaccess files, not just those for dirs that contain subdirs, to facilitate linking directly to files in the filesystem without first needing to retrofit the applicable .htaccess file.

web/**/.htaccess: Restrict redirection only of fully-existing paths, rather than of any path whose subdir exists, in order to avoid having to hardcode the absolute path to the directory containing the .htaccess file. This more restrictive approach still works because if the subdir exists and contains an .htaccess file, this (outer) .htaccess file's RewriteRules will be ignored completely until the inner .htaccess file's rules have been run, so that any subdir redirects will happen first. This "hole-punch" effect causes an existing filesystem path to always take priority over a virtual path (i.e. a redirect) defined in an outer .htaccess file.

Added web/datasources/ symlink to inputs/

web/servers/vegbiendev/fs: Updated symlink for new web/ dir nesting level

Deleted no longer used www/

Renamed www/ back to web/

Removed www/logs/ because it was actually successfully moved into main/ (but some of its files weren't)

Added www/logs/

web/: Moved auxiliary files into the main/ subdir in preparation for having just the web/ dir. Renamed web/ to www/ so it can be replaced with web/main/.

web/main/servers/vegbiendev/: Split it into db and fs forks, with db being the default. The fs fork links directly to /home/bien/svn on vegbiendev, which makes world-readable files directly web-accessible. (Permissions on /home/bien/svn and subdirs have been checked to ensure that private files are not world-readable.)

Added web/main/IH/db/