added .htaccess files for inputs/, schemas/ because these reside outside the DOCUMENT_ROOT, and therefore need an explicit RewriteBase directive so that RewriteRules in their subdirs can construct self-referential URLs. this ensures that the input URLs to RewriteRules are always URL paths instead of filesystem paths, which tend to mess up the redirects. (mod_rewrite is capable of doing filesystem-only redirects, but the associated RewriteRules require special care to ensure they match and reconstruct the filesystem path properly.) the presence of filesystem paths in RewriteRule inputs had been causing numerous bugs, especially in rules that use %{REQUEST_URI}, and the addition of the RewriteBases will hopefully avoid these types of bugs in the future. note that every path that resides outside the DOCUMENT_ROOT needs an explicit RewriteBase in its top-level .htaccess.
schemas/VegCore/VegCore.ERD.mwb: ensured that inheritance relationships are drawn as 1:1
web/**/.htaccess: appended query strings for external redirects: just use ? rather than ?& when an external redirect will be perfomed, because no dotpath parsing will be performed on the query string first (which would necessitate the & if the new query string looks like a dotpath)
schemas/VegCore/VegCore.ERD.png: Regenerated again because some tables were highlighted when it was exported, causing the highlighting to appear in the PNG
schemas/VegCore/VegCore.ERD.mwb: Regenerated exports
schemas/VegCore/VegCore.ERD.mwb: shortened embedded ERD URL using new abbreviations
web/**/.htaccess: RewriteRules: ensured flags are in alphabetical order
removed no longer needed web/dotpath.php. use web/.htaccess's parse-dotpath RewriteRule instead.
web/.htaccess: parse dotpath in query string: moved parsing from dotpath.php to RewriteRules. with the eventual addition of config env vars, this makes it possible for subdirs to configure their own dotpath parsing, rather than having all levels of the dotpath translated to a URL path. (for inner levels, it may el.g. be more appropriate to parse the dotpath as query params or pass it along to an external URL.) note that it takes only two lines of mod_rewrite (plus a workaround RewriteRule) to replace over a dozen lines of PHP code.
web/.htaccess: renamed REQUEST_URI_no_/ to REQUEST_URI_no_extra_/ to clarify that only an excess / is removed
web/.htaccess: moved set REQUEST_URI_no_/ under translate subdomain to path because it needs to be set right before being used to be accurate
web/.htaccess: setting REQUEST_URI_no_/: use one RewriteCond instead of two since the regexps can be combined
web/.htaccess: parse dotpath in query string: removed dotpath auto-detection code because this is now handled by a separate RewriteRule
web/.htaccess: auto-detect dotpath in query string (having a . before any = ) and mark it using a leading . . this is done as a separate step so that the dotpath is already explicitly marked as such when it's parsed.
web/dotpath.php: just match the QUERY_STRING directly, excluding &, instead of splitting apart the QUERY_STRING and then matching the dotpath portion. this allows the resulting regexp to be used directly in a .htaccess file.
web/.htaccess: prepend dir name if it's part of the filename: support MultiViews filenames without the extension, by using a lookahead request -F instead of a regular -f
schemas/VegCore/.htaccess: added RewriteBase to support relative redirects. this enables auto-prepending dir name if it's part of the filename, e.g. VegCore/ERD.pdf -> VegCore/VegCore.ERD.pdf).
web/.htaccess: prepend dir name if it's part of the filename (this works only if the dir supports relative redirects and sets %{ENV:innermost_dir})
schemas/VegCore/VegCore.ERD.mwb: made matched_taxon and accepted_taxon inherit from taxon instead of qualified_taxon because they don't contain the cf_aff (cf_aff.vegpath.org; aka identificationQualifier) that makes a taxon qualified
schemas/VegCore/VegCore.ERD.mwb: removed occurrence table, because it's really a synonym for taxon_occurrence ("specimen, observation, etc." <http://rs.tdwg.org/dwc/terms/#Occurrence>)
schemas/VegCore/VegCore.ERD.mwb: added labels for the left and right halves (event and occurrence). rearranged tables to help separate event- and occurrence-related tables.
schemas/VegCore/VegCore.ERD.mwb: rearranged to leave more space for location_observation, and to put all event-related fields on the left and occurrence-related fields on the left
web/.htaccess: parse dotpath in query string: heuristically detect query strings that don't contain dotpaths (such as mod_autoindex sort conditions), rather than always interpreting the part before the first & as the dotpath. now, the part before the first & will be interpreted as a dotpath if it has a . before any = . (query param names containing . are rare, so this usually works correctly.) note that you can always prepend . to force a dotpath, or & to force a query param.
web/dotpath.php: remove any . prefix which forces interpretation as a dotpath
schemas/VegCore/VegCore.ERD.mwb: taxon_concept: renamed source to according_to
schemas/VegCore/VegCore.ERD.mwb: removed no longer used images from zip archive using `zip -d`. this needs to be done every time an image is deleted from the diagram to remove it from the archive (and reclaim the unused space, since `zip -d` will also shrink the archive). note that you can't just expand and re-zip the files, because there is a header of some sort that indicates to MySQL Workbench that it's a valid .mwb file.
bugfix: schemas/VegCore/VegCore.ERD.mwb: also fixed inheritance relationships to the record table to be 1:1 (by search-and-replacing and then updating document.mwb.xml in the .mwb zip archive using `zip -u`). added separate legend for relationships and connector styles, which now uses example tables instead of screenshot images to ensure accurate sizing at all ERD zoom levels.
bugfix: schemas/VegCore/VegCore.ERD.mwb: fixed inheritance relationships to be 1:1 with optional participation by the derived table, rather than the incorrect 1:many relationshipwhich MySQL Workbench defaults to. (in OOP, each derived instance has its own instance of the base class, because it is a separate object.)
web/**/.htaccess: When there is no external redirect for the directory without the trailing /, instead auto-add the trailing / to ensure mod_autoindex relative links work properly. This must be done manually because the top-level .htaccess will not auto-add the trailing / if the dir has an .htaccess file (to allow the custom external redirects). There are actually only two .htaccess files that this applies to (web/.phpPgAdmin/.htaccess, .phpMyAdmin/.htaccess), indicating that dirs which have any kind of virtual paths (redirects) almost always have a "root" redirect when there is no specific subpath. This root redirect is intended to link to the datasource's own index of its available resources, e.g. the list of tables for a database source.
removed web/aggregators/.htaccess because it was only there to auto-add the trailing /, but this is now done by web/.htaccess
bugfix: web/.htaccess: auto-add trailing /: %{LA-F:REQUEST_FILENAME} lookaheads don't work, because they do not show the externally redirected URL, so we need to use an alternate mechanism instead, which just assumes that any dir containing an .htaccess file may contain a redirect and ignores just those dirs (subdirs are not ignored and will receive a trailing / as expected). To create the trailing / effect when you have a .htaccess without an external redirect, you need to manually tell it to correct the path for just that dir without the / (i.e. match ^/ , because a trailing / causes mod_rewrite to use an absolute filesystem path instead).
web/.htaccess: moved auto-add trailing / to after don't rewrite existing dirs, so that the path will automatically not be rewritten if it contains a trailing / and is a dir
web/.htaccess: don't rewrite existing paths: only prevent existing dirs with trailing / from being rewritten, because dirs without trailing / may be redirected
removed web/**/.htaccess whose only purpose was to auto-add the trailing / (which is now handled by the top-level .htaccess)
web/**/.htaccess: removed no longer needed auto-add of trailing / , which is now implemented for all dirs by the top-level .htaccess
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
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
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 / .
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.
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).
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 /
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.
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)
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)
README.TXT: umask: Removed -S because this causes the new umask to be echoed, and is not needed even when setting a symbolic umask
README.TXT: Datasource setup:: added step to use umask to prevent files from becoming web-accessible
README.TXT: Testing: what to put in your .profile: added `umask -S ug=rwx,o=` to prevent files from becoming web-accessible
README.TXT: fixed leading whitespace
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/
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
