added web/people/Brad_Boyle/morphosp symlink to morphospecies
added web/people/Brad_Boyle/morphospecies redirect to Morphospecies and scope.eml.txt
added web/people/Brad_Boyle/Morphospecies and scope.eml.txt symlink
added web/people/Brad_Boyle/TNRS redirect to Modifications to procedure to scrubbing names using TNRS.docx
added web/people/Brad_Boyle/Modifications to procedure to scrubbing names using TNRS.docx symlink
web/username_prefix.php: transposes: removed recommendation for vertical alignment because different quoting syntaxes, etc. make it difficult to have a consistent alignment anyway
web/username_prefix.php: remove padding used to visually separate elements: documented that this leaves embedded _ (eg. x_y) untouched
web/username_prefix.php: remove padding used to visually separate elements: documented that this also removes a leading __ that indicates an internal field
web/links/index.htm: updated to Firefox bookmarks: Quick links: added VegBIEN data dictionary spreadsheet, TNRS data dictionary.
fix: web/username_prefix.php: transposes: changed recommended syntax to y~x@url so that _y~ lines up vertically with [y] paths
web/username_prefix.php: removed special category comments syntax because this is now handled by transposes and insertion comments
web/username_prefix.php: added support for transposes ( y~x_@url -> x_y@url , Y~x@url -> xY@url ), which can be used to put the category in a column name first without duplicating the category
web/username_prefix.php: removed linewraps code because Google spreadsheets no longer supports wrapping on a - , and because a shorter syntax for category comments is now available
web/username_prefix.php: category comments: moved _-_ outside [] in comparison example since it will be deleted separately
bugfix: web/username_prefix.php: category comments: need /__/ around regexp
web/username_prefix.php: category comments: added support for a shorter syntax than [x_-_]y@url : x+y@url -> y@url
web/links/index.htm: updated to Firefox bookmarks: WebEx: added steps to join a test meeting. pg_restore: documented that you need to create the schema before you restore into it, or else you will get a cryptic error message that it's using pg_catalog instead. added Homebrew links, including instructions for setting psycopg2 up with it. added PostGIS links. username URLs: documented how to enable these in Internet Explorer. TWiki: documented what to do when moving the TWiki install dir.
bugfix: web/.phpPgAdmin/.htaccess: : handlers: use `chain` to only run them when the RewriteRule they apply to is run
web/.phpPgAdmin/.htaccess: schema : handler: removed `env=subject:schema` because that has already been set
web/.phpPgAdmin/.htaccess: tables: added : suffix handler
bugfix: web/.phpPgAdmin/.htaccess: view : match: moved to right after `view=` because it only applies to views, not functions
web/.phpPgAdmin/.htaccess: schema: page: indicate by prefixing with : to avoid needing to explicitly list all possible pages
web/.phpPgAdmin/.htaccess: table: action: indicate by prefixing with : to avoid needing to explicitly list all possible actions
web/util.js: removed no longer used parse_dot_path(), etc. this is handled by web/.htaccess instead.
web/index.php: Brad: added attribution/
web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.
web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs
added web/people/Brad_Boyle/identifiers
bugfix: web/index.php: Brad: updated resource names to match filesystem
bugfix: web/index.php: Brad: fixed URL base
web/index.php: sources: reordered/recategorized to match the subdirs and wiki.vegpath.org/VegCore
merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
added web/people/Brad_Boyle/identifier_examples, which is used by the VegBIEN data dictionary
placed web/BIEN3/TWiki/lib/LocalSite.cfg under version control because it contains absolute paths that need to be maintained
web/main.conf: updated paths
web/people/Brad_Boyle/*/.htaccess: set the destination filename using RewriteRule env, to allow escaping " " with "\ " instead of the difficult-to-read "\%20"
web/people/Brad_Boyle/*/.htaccess: use relative paths to new symlinks to avoid hardcoding paths
web/BIEN3/TWiki/twiki.conf: updated paths
web/people/Brad_Boyle/: added symlinks to Brad's files that are used in the data dictionaries
schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/
schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
web/BIEN3/Redmine/svn/.htaccess: removed unneeded RewriteBase because this does not use a relative redirect with ../
web/BIEN3: link to Redmine instead of directly to the wiki, since the Redmine/ dir should manage where BIEN3 default-redirects to
web/.fs: changed to point directly to the svn root, so that the VegBIEN dir does not contain any recursive symlinks
web/links/index.htm: updated to Firefox bookmarks: oXygen XML editor: added download link for the version (13.2) that works with NCEAS's license. bash: added fix to enable Ctrl+Arrow to work. GVFS: added links for file permissions bug. iPlant: added Atmosphere/Data Store links. Quick links: updated vegpath.org link to `vegpath.org.`.
web/username_prefix.php: username/password prompt message: added instructions to always append "." when visiting the homepage of the site ("vegpath.org.")
web/username_prefix.php: deletion comments: require ... strikethrough on both () to avoid ambiguity when the deleted part starts or ends with -
web/username_prefix.php: deletion comments: also support strikethrough syntax for clarity: (c_)x@url -> c_x@url
web/username_prefix.php: insertion comments: documented that the semantic meaning of the [] portion also applies, even though it's not included in the linked term name
web/username_prefix.php: added support for deletion comments of the form (c_)x(_d)@url -> c_x_d@url . deletion indicates that the semantic meaning of the () portion does not apply, even though it's included in the linked term name.
web/username_prefix.php: comments: use [] instead of () because in writing, [] denotes insertion, while () (as an editing mark) denotes something to remove
bugfix: web/index.php: fixed bug where full directory index would not display correctly if invoked as /index.php instead of / (caused by incorrect URL)
web/username_prefix.php: word-wraps: renamed to linewraps
web/username_prefix.php: added support for word-wraps of the form x_-_.y@url -> x.y@url (the _ are needed to work in Google spreadsheets)
bugfix: web/username_prefix.php: comments: need to use syntax that doesn't use : because Firefox will not update the "password" for the website with the new value after the : . the new syntax use () instead.
web/username_prefix.php: comment prefixes: support embedded ":" in comment
web/username_prefix.php: user2path(): comment prefixes: documented how to put the comment on a separate line when word-wrapping (c-_:x@url). this format works in Google spreadsheets.
web/username_prefix.php: user2path(): added support for comment prefixes, which can be used to include term categories. note: when URL is used without http:// , you must include a non-letter in the comment (eg. c_:x@url) to work in Firefox.
web/username_prefix.php: user2path(): visually separated steps for easier readability
bugfix: web/username_prefix.php: user2path(): padding used to visually separate 1st element of URL: require all padding to be __ because sometimes terms contain a leading or trailing _
bugfix: web/username_prefix.php: user2path(): padding used to visually separate 1st element of URL: support embedded @ inside highlighted part: also need to match end-padding when followed by "."
web/username_prefix.php: user2path(): padding used to visually separate 1st element of URL: support embedded @ inside highlighted part
web/username_prefix.php: user2path(): added support for padding used to visually separate 1st element of URL (x@url -> x@url)
bugfix: web/username_prefix.php: need to handle : in login (which would normally indicate a password)
web/.htaccess: auto-detect dotpath: need to explicitly set usernames_disabled=1, because for some reason the `%{QUERY_STRING} =""` check doesn't detect a query string
web/.htaccess: auto-detect dotpath: removed handling of no longer used @ prefix (used to be used by username-based prefix subpaths)
bugfix: web/.htaccess: username-based prefix subpaths: usernames_disabled: also need to support it being set in the current round
bugfix: web/.htaccess: username-based prefix subpaths: removed support for query strings because these are often used at the root level, and should then be treated as a regular dotpath rather than something with a username-based prefix
bugfix: web/.htaccess: forced mod_autoindex listing: use $usernames_disabled to ensure that usernames stay disabled even when /all path is removed
bugfix: web/.htaccess: username-based prefix subpaths: added back usernames_disabled env var, because it is needed if a RewriteRule in a previous round creates an empty path (mod_rewrite runs the RewriteRules repeatedly until no replacements are made)
bugfix: web/.htaccess: username-based prefix subpaths: REDIRECT_REQUEST_URI: also allow it to be unset, as it is when using usernames
fix: web/index.php: directory index: don't append QUERY_STRING, as this is not used by /all
web/.htaccess: username-based prefix subpaths: removed usernames_disabled env var because the bug that appeared to require this has now been fixed
bugfix: web/.htaccess: username-based prefix subpaths: also need to check original URL (REDIRECT_REQUEST_URI), in addition to current URL (REQUEST_URI) to see if usernames should be disabled
web/.htaccess: username-based prefix subpaths: allow explicitly disabling in a RewriteRule to handle special cases
bugfix: web/index.php: directory index: use QUERY_STRING, not HTTP_AUTHORIZATION (HTTP_AUTHORIZATION was probably left over from a previous attempt to provide username-based prefix subpaths)
web/.htaccess, username_prefix.php: username-based prefix subpaths: don't require the // at the end , to avoid clutter. IMPORTANT: in order to access the home page after visiting a URL with a username, you must now append "." to the host ("vegpath.org.") (other pages are not affected by this problem). since vegpath.org is a URL shortener, this is a worthwhile tradeoff to avoid needing the // suffixes everywhere.
bugfix: web/.htaccess: subdomains: each path element must be non-empty, to avoid matching a trailing . incorrectly
web/.htaccess: username-based prefix subpaths: updated documentation to use leading // instead of trailing ? or ?@
web/username_prefix.php: $_SERVER["PHP_AUTH_USER"] test: factored $_SERVER["SCRIPT_URL"] out of both branches of if statement
web/username_prefix.php: don't remove @ from query string because that is no longer a special character
fix: web/.htaccess: username-based prefix subpaths: changed format to subpath@host//path because the trailing ? makes it look like the sentence the URL is in is a question
web/.phpPgAdmin/.htaccess: action redirect: only append ? if adding to the query string
web/.phpPgAdmin/.htaccess: view: default to displaying the columns rather than the definition
web/.phpPgAdmin/.htaccess: support viewing the columns of a view rather than the definition
web/.phpPgAdmin/.htaccess: RewriteRules: use overridable action var
web/.phpPgAdmin/.htaccess: support overriding action param in a later RewriteRule
web/.phpPgAdmin/.htaccess: removed skip= because this creates a confusing control flow, and prevents using chain
web/.htaccess: auto-detect dotpath in query string: also auto-prepend & for query strings appended to a username-based prefix, so that these don't need to have & manually prepended to make them appendable
web/.htaccess: auto-detect dotpath in query string: also auto-detect dotpath for query strings appended to a username-based prefix, so that these don't need to have . prepended to make them appendable
