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# Date Author Comment
8478 04/14/2013 01:27 AM Aaron Marcuse-Kubitza

web/.htaccess: auto-add trailing / if not external redirect: added test if `%{REQUEST_FILENAME} -d` in addition to checking %{LA-F:REQUEST_FILENAME}, because there are some cases (e.g. subdirs that are symlinked outside the DOCUMENT_ROOT) where LA-F:REQUEST_FILENAME for some reason appends /home to the REQUEST_FILENAME, but the current REQUEST_FILENAME is fortunately already a dir and can be checked directly

8477 04/14/2013 01:07 AM Aaron Marcuse-Kubitza

web/.htaccess: auto-add trailing / if not external redirect: removed no longer applicable comment that dir without trailing / is provided as an absolute filesystem path, because this is only true in inner .htaccess files for their top-level dirs

8476 04/14/2013 01:01 AM Aaron Marcuse-Kubitza

bugfix: web/.htaccess: auto-add trailing / if not external redirect: match any path that does not end in / (and satisfies the -d lookahead), rather than only absolute filesystem paths, which are only applicable in inner .htaccess files (and even then only for the outermost dir they control) but not in the top-level .htaccess file. Note that the inner .htaccess files can still use ^/ to match their own dir, just not their subdirs, without a trailing / .

8475 04/14/2013 12:25 AM Aaron Marcuse-Kubitza

bugfix: web/.htaccess: auto-add trailing / if not external redirect: replace with "%{REQUEST_URI}/" instead of the empty string (which gets auto-translated to have a trailing /), because the empty string only works in the top-level dir of the .htaccess file (it redirects to the RewriteBase, which ends in /). The entire REQUEST_URI is needed to do the auto-add in dirs which do not have their own auto-add trailing / rule. Also, using REQUEST_URI avoids the need to (sometimes) set RewriteBase for use by relative URLs in replacement strings, because this is an absolute URL instead. Setting RewriteBase manually is best avoided, because it hardcodes the URL path to the .htaccess file, which may change.

8474 04/14/2013 12:17 AM Aaron Marcuse-Kubitza

bugfix: web/.htaccess: auto-add trailing / if not external redirect: use "%{LA-F:REQUEST_FILENAME} d" instead of "$0 -F" so that the actual value of REQUEST_FILENAME tested, and $0 can also match strings which are not file paths. This is because only those no-trailing/-paths which did not match the RewriteBase are provided to mod_rewrite as absolute filepaths, but RewriteBase is not an issue in the outermost .htaccess (because the RewriteBase is / , which is always matched). This means the method of testing for ^/ to match a no-trailing-/-path will only work in inner .htaccess files (where it is currently used extensively).

8473 04/13/2013 05:47 PM Aaron Marcuse-Kubitza

web/.htaccess: bugfix: moved auto-add trailing / if not external redirect to before don't rewrite existing paths because the trailing / also needs to be added on paths which are existing paths, but are just missing the trailing /

8472 04/13/2013 06:37 AM Aaron Marcuse-Kubitza

web/.htaccess: auto-add trailing / if not external redirect (limited form of DirectorySlash). this allows URLs without trailing /, for dirs which have a special external redirect to the datasource's homepage when there is no trailing /, but still auto-adds the trailing / for all other dirs.

8471 04/13/2013 06:17 AM Aaron Marcuse-Kubitza

README.TXT: Debugging: mod_rewrite: cached redirects issue: changed to limit the cache clearing to when a DirectorySlash-related redirect is changed, since only those redirects are permanent, not the RewriteRule redirects (unless you explicitly set them as permanent)

8470 04/13/2013 06:03 AM Aaron Marcuse-Kubitza

README.TXT: Debugging: mod_rewrite: added tip that whenever you change a RewriteRule, you must clear your browser's cache to ensure that a cached redirect is not used instead (temporary redirects are not supposed to be cached, but sometimes Firefox caches them anyway)

8469 04/13/2013 04:41 AM Aaron Marcuse-Kubitza

README.TXT: umask: Removed -S because this causes the new umask to be echoed, and is not needed even when setting a symbolic umask

8468 04/13/2013 04:18 AM Aaron Marcuse-Kubitza

README.TXT: Datasource setup:: added step to use umask to prevent files from becoming web-accessible

8467 04/13/2013 04:16 AM Aaron Marcuse-Kubitza

README.TXT: Testing: what to put in your .profile: added `umask -S ug=rwx,o=` to prevent files from becoming web-accessible

8466 04/13/2013 04:05 AM Aaron Marcuse-Kubitza

README.TXT: fixed leading whitespace

8465 04/13/2013 02:46 AM Aaron Marcuse-Kubitza

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.

8464 04/13/2013 02:41 AM Aaron Marcuse-Kubitza

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

8463 04/13/2013 02:28 AM Aaron Marcuse-Kubitza

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" "$@"`

8462 04/13/2013 02:11 AM Aaron Marcuse-Kubitza

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

8461 04/13/2013 02:10 AM Aaron Marcuse-Kubitza

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.

8460 04/13/2013 01:49 AM Aaron Marcuse-Kubitza

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

8459 04/13/2013 01:44 AM Aaron Marcuse-Kubitza

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

8458 04/13/2013 01:34 AM Aaron Marcuse-Kubitza

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)

8457 04/11/2013 10:29 PM Aaron Marcuse-Kubitza

Moved validation/ under planning/workflow/

8456 04/11/2013 10:28 PM Aaron Marcuse-Kubitza

Moved planning/use_cases/ under planning/goals/

8455 04/11/2013 10:26 PM Aaron Marcuse-Kubitza

Moved planning/milestones/ under planning/timeline/

8454 04/11/2013 10:23 PM Aaron Marcuse-Kubitza

Added inputs/VegBIEN/planning shortcut to fs/planning

8453 04/11/2013 10:16 PM Aaron Marcuse-Kubitza

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

8452 04/11/2013 10:14 PM Aaron Marcuse-Kubitza

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

8451 04/11/2013 05:56 PM Aaron Marcuse-Kubitza

Added web/.gbif shortcut to datasources/GBIF

8450 04/11/2013 04:52 PM Aaron Marcuse-Kubitza

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

8449 04/11/2013 04:30 PM Aaron Marcuse-Kubitza

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

8448 04/11/2013 02:45 PM Aaron Marcuse-Kubitza

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).

8447 04/11/2013 02:34 PM Aaron Marcuse-Kubitza

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.

8446 04/11/2013 02:07 PM Aaron Marcuse-Kubitza

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.

8445 04/11/2013 01:56 PM Aaron Marcuse-Kubitza

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.)

8444 04/11/2013 01:36 PM Aaron Marcuse-Kubitza

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).

8443 04/10/2013 11:17 PM Aaron Marcuse-Kubitza

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)

8442 04/10/2013 10:20 PM Aaron Marcuse-Kubitza

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

8441 04/10/2013 10:18 PM Aaron Marcuse-Kubitza

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.

8440 04/10/2013 10:15 PM Aaron Marcuse-Kubitza

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.

8439 04/10/2013 10:11 PM Aaron Marcuse-Kubitza

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

8438 04/10/2013 09:42 PM Aaron Marcuse-Kubitza

Added web/people/

8437 04/10/2013 09:08 PM Aaron Marcuse-Kubitza

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

8436 04/10/2013 09:07 PM Aaron Marcuse-Kubitza

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

8435 04/10/2013 09:03 PM Aaron Marcuse-Kubitza

Added schemas/VegCore/.htaccess

8434 04/10/2013 08:57 PM Aaron Marcuse-Kubitza

Added web/.vegcore shortcut to exchange_schemas/VegCore

8433 04/10/2013 08:34 PM Aaron Marcuse-Kubitza

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

8432 04/10/2013 08:28 PM Aaron Marcuse-Kubitza

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 /)

8431 04/10/2013 08:25 PM Aaron Marcuse-Kubitza

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

8430 04/10/2013 08:19 PM Aaron Marcuse-Kubitza

Added web/.fs symlink to .vegbiendev/fs

8429 04/10/2013 01:53 PM Aaron Marcuse-Kubitza

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.

8428 04/10/2013 01:47 PM Aaron Marcuse-Kubitza

Added web/.nimoy, .vegbiendev shortcuts

8427 04/10/2013 01:44 PM Aaron Marcuse-Kubitza

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

8426 04/10/2013 01:39 PM Aaron Marcuse-Kubitza

Moved web/TCS/ to schemas/

8425 04/10/2013 01:36 PM Aaron Marcuse-Kubitza

Added web/exchange_schemas/ symlink

8424 04/10/2013 01:35 PM Aaron Marcuse-Kubitza

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

8423 04/10/2013 01:34 PM Aaron Marcuse-Kubitza

Added schemas/.htaccess

8422 04/10/2013 01:33 PM Aaron Marcuse-Kubitza

Added web/exchange_schemas/

8421 04/10/2013 01:28 PM Aaron Marcuse-Kubitza

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

8420 04/10/2013 01:19 PM Aaron Marcuse-Kubitza

Moved web/BIEN2, IH into aggregators/

8419 04/10/2013 01:18 PM Aaron Marcuse-Kubitza

Moved web/BIEN2, IH into aggregators/

8418 04/10/2013 01:09 PM Aaron Marcuse-Kubitza

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

8417 04/10/2013 01:04 PM Aaron Marcuse-Kubitza

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

8416 04/10/2013 01:01 PM Aaron Marcuse-Kubitza

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

8415 04/10/2013 12:59 PM Aaron Marcuse-Kubitza

Added inputs/.TNRS/.htaccess

8414 04/10/2013 12:13 PM Aaron Marcuse-Kubitza

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

8413 04/10/2013 12:12 PM Aaron Marcuse-Kubitza

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

8412 04/10/2013 10:14 AM Aaron Marcuse-Kubitza

web/VegBIEN/: Moved to datasources/

8411 04/10/2013 10:07 AM Aaron Marcuse-Kubitza

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 /.)

8410 04/10/2013 09:48 AM Aaron Marcuse-Kubitza

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

8409 04/10/2013 09:45 AM Aaron Marcuse-Kubitza

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

8408 04/10/2013 09:40 AM Aaron Marcuse-Kubitza

inputs/SALVIAS/.htaccess: Removed test RedirectMatch directive

8407 04/10/2013 09:38 AM Aaron Marcuse-Kubitza

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.

8406 04/10/2013 07:49 AM Aaron Marcuse-Kubitza

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

8405 04/10/2013 06:15 AM Aaron Marcuse-Kubitza

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.

8404 04/10/2013 05:59 AM Aaron Marcuse-Kubitza

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

8403 04/10/2013 05:15 AM Aaron Marcuse-Kubitza

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

8402 04/10/2013 05:12 AM Aaron Marcuse-Kubitza

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)

8401 04/10/2013 03:33 AM Aaron Marcuse-Kubitza

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.

8400 04/10/2013 03:29 AM Aaron Marcuse-Kubitza

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

8399 04/10/2013 03:28 AM Aaron Marcuse-Kubitza

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

8398 04/10/2013 03:28 AM Aaron Marcuse-Kubitza

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

8397 04/10/2013 03:21 AM Aaron Marcuse-Kubitza

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

8396 04/10/2013 01:46 AM Aaron Marcuse-Kubitza

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

8395 04/10/2013 01:44 AM Aaron Marcuse-Kubitza

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

8394 04/10/2013 12:15 AM Aaron Marcuse-Kubitza

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).

8393 04/09/2013 10:59 PM Aaron Marcuse-Kubitza

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

8392 04/09/2013 10:55 PM Aaron Marcuse-Kubitza

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

8391 04/09/2013 10:47 PM Aaron Marcuse-Kubitza

Added wiki shortcut to Redmine/wiki

8390 04/09/2013 10:43 PM Aaron Marcuse-Kubitza

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

8389 04/09/2013 10:41 PM Aaron Marcuse-Kubitza

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)

8388 04/09/2013 10:11 PM Aaron Marcuse-Kubitza

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

8387 04/09/2013 10:10 PM Aaron Marcuse-Kubitza

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.

8386 04/09/2013 10:01 PM Aaron Marcuse-Kubitza

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

8385 04/09/2013 09:48 PM Aaron Marcuse-Kubitza

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

8384 04/09/2013 09:36 PM Aaron Marcuse-Kubitza

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.

8383 04/09/2013 09:33 PM Aaron Marcuse-Kubitza

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.

8382 04/09/2013 09:23 PM Aaron Marcuse-Kubitza

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

8381 04/09/2013 09:13 PM Aaron Marcuse-Kubitza

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)

8380 04/09/2013 09:11 PM Aaron Marcuse-Kubitza

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

8379 04/09/2013 04:37 PM Aaron Marcuse-Kubitza

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