web/main/.phpMyAdmin/.htaccess: Prepend http:// to the dest URL stem, instead of requiring the dest URL to provide the protocol, because the two // are replaced with one / by Apache when mod_rewrite is on, creating an invalid URL

web/main/.htaccess: translate dotpaths: Fixed bug where can't remove all [] escapes, because this would also remove [] from protected parts of the URL (i.e. before the last /). Instead just remove up to two [] escapes per dot-level, e.g. a.[b.c]=[d.e] -> a/b.c=d.e . Note that this removes the restriction against URLs containing "[]", because these [] will be left as-is as long as they are followed at some point by a / .

Removed web/.htaccess because it is not part of any site (web/main/.htaccess is the top-level .htaccess file for the default site)

web/main/.htaccess: translate dotpaths: replace all unescaped . with / : Allow empty components on either side of the . , to ensure that all unescaped dots are consistently replaced with / . Note that hidden directories that start with . will have the . preserved, because they have (or get) a trailing slash, which prevents dotpath from operating on them.

web/main/.htaccess: translate dotpaths: remove all [] escapes: Also remove empty [] to allow permalinking clients to easily generate escaped strings by URL-encoding the value and enclosing it in [], which will now also work even if the value is empty. This change will break any destination URLs that use "[]", such as PHP scripts that use this to indicate an array variable in the query string. In these URLs, the [] must now be %-encoded.

web/main/.htaccess: RewriteRules with [redirect] and http:// : Removed [redirect] because it is implied when the replacement is an absolute URL

web/main/.htaccess: RewriteRules with [redirect]: Added last because apparently redirect will not immediately cause the redirect, and will instead continue rewriting the URL ("You will almost always want to use [R] in conjunction with [L] (that is, use [R,L]) because on its own, the [R] flag prepends http://thishost[:thisport] to the URI, but then passes this on to the next rule in the ruleset, which can often result in 'Invalid URI in request' warnings." <http://httpd.apache.org/docs/2.2/rewrite/flags.html#flag_r&gt;)

web/main/.htaccess: RewriteRules: Added [discardpath,noescape] flags to all rules, because these are needed for correct interpretation of the replacement and should be the default setting. For some rules they may be optional, but it is better to include them on all rules to ensure there is never an unexpected effect from omitting them.

web/main/.htaccess: Added "RewriteOptions inherit" because this¹ should be the default setting, to ensure that global filter rules also occur in subdirs. Note that the presence of this directive in this .htaccess file does not solve this problem, but putting it there will remind writers of subdir .htaccess files that they need to include that directive....

web/main/SALVIAS/.htaccess: RedirectMatch for below top-level: Use /(.*?)/?$ suffix for consistency with other sources' RedirectMatch patterns

web/main/TCS,VegX/.htaccess: Fixed bug where need to match dirs by themselves in addition to when followed by a filename

web/main/DwC/.htaccess: Fixed bug where need to match dirs by themselves (/DwC/, /DwC/history/) in addition to when followed by a filename

web/main/.htaccess: mod_rewrite: Removed unneeded RewriteBase, because the default setting for RewriteBase is actually the dir of the .htaccess file itself, rather than always / . ("RewriteRule can be used in per-directory config files (.htaccess). There it will act locally, i.e., the local directory prefix is stripped at this stage of processing and your rewriting rules act only on the remainder. At the end it is automatically added back to the path." <http://httpd.apache.org/docs/1.3/mod/mod_rewrite.html#RewriteBase&gt;)

web/main/SALVIAS/*/.htaccess: Added trailing / to Redirect paths, which works now that a trailing / is automatically added to all paths by dotpath translation

web/main/SALVIAS/: Moved db/ and users/ actions to their corresponding subdirs. The rules will still be run in the appropriate order, because if a .htaccess exists in a subdir, it will be used in preference to the .htaccess in the parent dir.

my2pg: Removed SETs for standard_conforming_strings, escape_string_warning because these are also prepended by my2pg.data, which this script's output is piped to

my2pg.data: \0 removal: Fixed bug where need to handle all backslashes before the 0, because they might escape just each other (an even number of \) rather than also encoding the \0 (an odd number of \)

web/main/.htaccess: translate dotpaths to /-paths: Added examples

web/main/.htaccess: translate dotpaths to /-paths: Translate all .-separated components in the path to / instead of just those that exist in the filesystem. This allows per-source rules to match just a / for the path-element separator instead of sometimes / and other times . (depending on whether that portion of the dotpath had been translated). Support [] escapes that preserve any . they surround, e.g. a.[b.c] -> a/b.c . (Supporting []-escapes requires that the /-path be "sealed" by appending a / , to prevent the . -> / translation rule from reinterpreting a newly-unescaped [] sequence as a dotpath. This also requires that the translation rule ignore anything before the last /, because it could have been []-unescaped by a previous round of mod_rewrite, e.g. in another dir. All the per-source rules need to be retrofitted to support the new trailing / .) Note also the discardpath flag (http://httpd.apache.org/docs/2.2/rewrite/flags.html#flag_dpi) on all RewriteRules that perform a replacement on the input string (i.e. that have a pattern other than ^.*$). This flag is needed to avoid infinite loops, because otherwise, a critical bug in mod_rewrite causes it to reappend the filename portion of the input string (PATH_INFO) to the result, causing it to be present twice, e.g. a/b -> a/b/b (https://issues.apache.org/bugzilla/show_bug.cgi?id=38642).

web/main/nimoy/: Moved to web/main/servers/ so it can be grouped with other resources that are servers

web/main/index.php: $root: Fixed bug where need to use gethostbyaddr($_SERVER["SERVER_ADDR"]) instead of $_SERVER["SERVER_NAME"] because SERVER_NAME is actually set to whichever hostname the server is accessed through (e.g. path.vg or vegbiendev.nceas.ucsb.edu), rather than always being set to the reverse-DNS lookup of SERVER_ADDR, as is specified in the Apache docs ("If no ServerName is specified, then the server attempts to deduce the hostname by performing a reverse lookup on the IP address" <http://httpd.apache.org/docs/2.2/mod/core.html#servername&gt;)

web/main/.htaccess: Added back "don't rewrite existing paths" to ensure that rules after it will not rewrite any actual files (web page dependencies)

web/main/nimoy/.htaccess: Removed no longer needed trailing /

web/main/.phpMyAdmin/.htaccess: Add trailing / to provided URL in case the user didn't add it

web/main/nimoy/.htaccess: Removed unnecessary index.php from end of phpMyAdmin URL

web/main/DwC,SALVIAS,TCS,VegX: Added .htaccess redirects and dot-path-matching empty dirs, which will replace the index.php redirects with a simpler syntax (http://httpd.apache.org/docs/2.2/mod/mod_alias.html#redirect)

web/main/.htaccess: translate dot-paths to dirs: Documented that this only occurs when the dirs exist in the filesystem, and that each subdir Redirect directive needs a corresponding tree of (empty) dirs

Removed no longer used web/main/_archive/index.htm. Use web/main/index.php instead, which issues the Location: header to support clients other than web browsers.

web/vegpath/: Renamed to web/main/ because the content here is the main site hosted on vegbiendev. It will eventually contain internal links to VegBIEN resources in addition to external links (persistent URLs) to sources used in creating VegBIEN.

web/vegpath/.htaccess: Removed "don't rewrite existing paths" RewriteRule because there are no longer any rules after it that require it

web/vegpath/.htaccess: translate dot-paths to dirs: translate all levels of dot-paths present in the filesystem rather than just the first level, by using the [next] RewriteRule flag (http://httpd.apache.org/docs/current/rewrite/flags.html#flag_n). This avoids the need to translate further levels of dot-paths in each subdir's .htaccess.

web/vegpath/.htaccess: translate subdomain to path: Simplified using new subdomain2path RewriteMap, which avoids the need for a separate RewriteRule+RewriteConds for each number of nested subdomains

web/vegpath.conf: subdomain2path RewriteMap: Fixed bug where need `RewriteEngine on` in the VirtualHost config for a prg: RewriteMap to take effect ("External rewriting programs are not started if they're defined in a context that does not have RewriteEngine set to on." <http://httpd.apache.org/docs/current/rewrite/rewritemap.html#prg&gt;)

web/vegpath.conf: Added subdomain2path RewriteMap

Added web/subdomain2path for use by RewriteMap

web/vegpath.conf: Added spacing between sections and reordered directives

web/vegpath/.htaccess: translate 2-level subdomain to prefix: interpret subdomains in (standard) reverse instead of forward order (e.g. history.DwC instead of DwC.history)

web/vegpath/.htaccess: Don't also translate dash-paths to dirs (in addition to dot-paths) because this adds unnecessary complexity and was only used to allow expressing parts of subdomain paths in forward instead of reverse order (e.g. DwC-history instead of history.DwC)

web/vegpath/.htaccess: translate dot-/dash-paths to dirs: don't match / inside a . or - component, because it has a lower precedence

web/vegpath/.htaccess: translate dot-/dash-paths to dirs: changed comment to indicate that these rules can (eventually) translate any dot-/dash-path, not just the head

web/vegpath/.htaccess: translate subdomain to prefix: Use last to avoid further rewriting, since these rules make the destination a /-path

web/vegpath/.htaccess: Also translate dash-paths (e.g. DwC-history) to dirs

web/vegpath/.htaccess: translate both 1-level and 2-level subdomains to dir prefixes

web/vegpath/.htaccess: translate subdomain to prefix: HTTP_HOST RewriteCond: Don't capture part after . because it isn't used as a replacement (it used to be used for this when a now-unnecessary browser redirect was performed)

web/vegpath/.htaccess: don't rewrite existing paths: Moved before other RewriteRules so that page dependencies (such as util.js) can be loaded more quickly without needing to pass through all the rewrite rules first

web/vegpath/.htaccess: ErrorDocument: Use / instead of /index.php because index.php is the DirectoryIndex and doesn't need to be hardcoded

web/vegpath/.htaccess: translate subdomain to prefix: Fixed bug where can only run this is if the dest subdir has a .htaccess file, because this prevents the RewriteRule from being re-run for the subdir (which would lead to infinite recursion because the rule is not idempotent)

web/vegpath/.htaccess: translate subdomain to prefix: Fixed bug where need to prepend %{DOCUMENT_ROOT} to the file path when testing it for existence

web/vegpath/.htaccess: translate path head to dir (if the dir exists)

web/vegpath/.htaccess: translate subdomain to prefix: Set nosubreq to avoid infinite recursion (the RewriteRule is not idempotent)

web/vegpath/.htaccess: translate subdomain to prefix: Don't translate all nested subdomains, because some of them may result from the machine's own name (vegbiendev.nceas.ucsb.edu) and should not be removed. Instead, remove only the leftmost level of subdomain, and only if it corresponds to a filesystem directory.

web/vegpath/index.php: Use $alias whenever VegPath was reached via the machine's own name (vegbiendev.nceas.ucsb.edu) rather than via a shortened domain (path.vg), so that the right path root can seamlessly be used when path.vg is down

web/vegpath/.htaccess: Translate subdomain to path prefix

Added inputs/MO/_src/TropicosSpecimens_2013_03_12_*.txt.md5

Added inputs/MO/_archive

Added inputs/MO/_src/

web/vegpath/index.php: Brad-Boyle root: Fixed link

web/vegpath/index.php: CTFS root: Fixed link

web/vegpath/index.php: CTFS-schema: Use $Redmine_svn

web/vegpath/.htaccess: Remove www subdomain

Added web/logs/

web/vegpath/.htaccess: Use the simpler ErrorDocument directive instead of a catch-all RewriteRule to handle non-filesystem paths

web/vegpath/index.php: $alias: Use HTTP_HOST and SCRIPT_NAME so the alias doesn't need to be hardcoded

web/vegpath/util.php: Added ensure_prefix(), ensure_suffix()

web/vegpath/index.php: Switching back to path.vg now that the .vg root DNS is back online

web/vegpath/index.php: Use REQUEST_URI (removing the script's own dir) instead of PATH_INFO, to support being used for the Apache ErrorDocument directive

web/vegpath/.htaccess: mod_rewrite: Don't run any further rewrite rules if path exists, to avoid needing to add RewriteConds to each RewriteRule to check if the path exists

web/vegpath/index.php: Changed page title to contain "persistent URLs" because VegPaths are conceptually a type of PURL <http://en.wikipedia.org/wiki/PURL>

web/vegpath/index.php: $alias: Switching back to j.mp/vegpath# because the .vg root DNS server is down. (The .vg registrar adamsnames.com also displays an under construction page.) If the registrar stays down, we may want to switch a different top-level domain.

web/vegpath/.htaccess: DirectoryIndex: Removed index.htm because HTML files should not be used for redirection (they don't issue the Location: header needed by clients other than web browsers)

web/vegpath/.htaccess: mod_rewrite: Added `RewriteOptions inherit` so this .htaccess file can be copied to subdirs and will inherit the "unknown paths" rule

web/vegpath/index.php: Use $PATH_INFO (i.e. index.php/$PATH_INFO) instead of the query string to pass the path to index.php, so that the query string can be used for other things

web/vegpath/index.php: top-level path parsing: Use parse_dot_path() instead of parse_mixed_path() because XPaths are now (client-side) fragments, and don't need to be supported by the path mechanism

web/vegpath/index.php: SALVIAS: Don't append #Plot_ when there is no subpath

web/vegpath/index.php: SALVIAS: Factored out URL to $SALVIAS

web/vegpath/index.php: SALVIAS: Appended Plot_ to dest URL because both data dictionary sections start with this, so it doesn't need to be included in the VegPath

web/vegpath/index.php: XPath resources: Removed # at end of destination URL because the # is now part of the #/XPath suffix (and is added by the user)

web/vegpath/index.php: XPath resources: Added # before XPath because the XPath is actually a location within the resource, and thus resolvable by the client (or user) themselves, rather than part of the redirected URL (which only needs to forward to the XML schema file)

web/vegpath/index.php: Updated $alias to the newly-registered path.vg domain, which is shorter and more intuitive-looking than the previous value j.mp/vegpath (from bitly.com). Note that using a domain also allows redirects without JavaScript, which can be used by any web client (such as a Python script), not just a web browser.

web/vegpath/index.php: Renamed ref to ns to emphasize that the resources in this field are namespaces for the paths

web/vegpath/index.php: add_ref(): Renamed $suffix to $path_pat to distinguish it from the actual suffix string sent in the URL

web/vegpath/index.php: custom_separator(): Marked optional params as such

web/vegpath/index.php: Terms: IH-db: Factored out phpMyAdmin URL into $IH_db

web/vegpath/index.php: Terms: Added IH-db

web/vegpath/index.php: php*Admin(): Added support for a fixed table that doesn't need to be specified in the path

web/: Removed svn:executable permissions from non-executable files

web/vegpath/index.php: Data: Added Institutions subsection

web/vegpath/index.php: Placed Terms and Data sections side-by-side in two columns so that data resources would not need to come after a long list of terms resources

web/vegpath/main.css: Added .indent

web/vegpath/index.php: People: Added Brad's VegCore ID terms spreadsheets

web/vegpath/index.php: Factored Redmine svn URLs out into $Redmine_svn

Added schemas/VegCore/Brad_Boyle/ with Brad's VegCore IDs terms spreadsheets

web/vegpath/index.php: URL fragment redirect: Removed loading indicator (blinking of resource being loaded) because for file downloads, the download will not redirect to a new page and the resource name will instead remain blinking

web/vegpath/index.php: URL fragment redirect: Fixed bug where need to use parse_mixed_path() instead of parse_dot_path() to support XPaths

web/vegpath/index.php: Terms: Added CTFS

web/vegpath/index.php: URL patterns header: Reworded comment to clarify that the elements that can be left out are in italics

web/vegpath/index.php: URL fragment redirect: Only perform fragment redirect if URL shortener requires it (as indicated by the $alias ending in #)

web/vegpath/index.php: nimoy nodes: Factored nimoy phpMyAdmin() calls out into nimoy_db() function

web/vegpath/index.php: nimoy nodes: Factored nimoy URL prefix out into $nimoy

web/vegpath/index.php: SALVIAS: Added subnodes for each SALVIAS database on nimoy