moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).
web/links/index.htm: updated to Firefox bookmarks. added links to the sPlot ERD. Dropbox: added information about a missing upgrade notification when you use the Dropbox client to look up a file on the Dropbox website.
web/links/index.htm: updated to Firefox bookmarks. Quick links: removed page descriptions, which clutter up the quick links list.
web/links/index.htm: updated to Firefox bookmarks. Quick links: added VegBIEN FAQ.
web/links/index.htm: updated to Firefox bookmarks. Quick links: removed page descriptions, which clutter up the quick links list
web/links/index.htm: updated to Firefox bookmarks. Quick links: added link to meetings
web/links/index.htm: updated to Firefox bookmarks. Quick links: reordered in the order they should apper to visitors to the BIEN links page, rather than to me in the bookmarks toolbar.
web/links/index.htm: updated to Firefox bookmarks. updated favicons.
web/links/index.htm: updated to Firefox bookmarks. added links for sPlot and iPlant open-sourcing.
web/links/index.htm: updated to Firefox bookmarks. open-sourcing BIEN: added links for VegBank's license (GPLv2), and how these terms apply to us (a diff of our changes is not GPL-ed under GPLv2, although it is claimed to be GPL-ed under GPLv3)
web/links/index.htm: updated to Firefox bookmarks. added links for fixing the "App Store is temporarily unavailable" error (turn on Spotlight) and modifying a running shell script (unlink it first).
web/links/index.htm: updated to Firefox bookmarks. PostgreSQL: added links for troubleshooting out-of-memory errors, which show up (cryptically) as "The database system is in recovery mode" errors in processes running at the time the out-of-memory condition occurred.
web/links/index.htm: updated to Firefox bookmarks. added API writing links, including the best quotes from a Google developer's PowerPoint on the topic.
web/links/index.htm: updated to Firefox bookmarks. BIEN: added DataONE compatibility links.
web/links/index.htm: updated to Firefox bookmarks. BIEN: open-sourcing: added UArizona and iPlant IP policies, which are relevant to Brad's numerous documentation and schema-modeling contributions in our repository (most done while he was an iPlant employee).
web/links/index.htm: updated to Firefox bookmarks. BIEN: open-sourcing: added potential licenses we could use (public domain/CC0, BSD, GNU Verbatim Copying License, not CC-BY because incompatible w/ GPL).
web/links/index.htm: updated to Firefox bookmarks. BIEN: added links related to open-sourcing it, including the "Request to Open Source Software" form, the funding sources that need to be included in it, and part of the delegation of authority chain (from the UC Regents) that authorizes the open-sourcing.
web/links/index.htm: updated to Firefox bookmarks. upgrading to PostgreSQL 9.3: added Linux pg_upgrade steps and install instructions. added Mac PostGIS, psycopg2 install steps. added note that after installing, you need to restore config values that the upgrade reset: in pgAdmin > Preferences > Query tool > Query editor, set Max characters per column back to -1 (to avoid cells being truncated). (this is not a bug in PostgreSQL, only in pgAdmin, and does not signal a need to downgrade.)
bugfix: lib/Firefox_bookmarks.reformat.csv: remove empty <DD> tags (which Firefox now adds for all bookmarks) so they don't create a blank space on the page
bugfix: lib/Firefox_bookmarks.reformat.csv: don't prepend "page's description:" to empty <DD> tags, which Firefox now adds for all bookmarks, even if they don't have a description
web/links/index.htm: updated to Firefox bookmarks. added instructions for upgrading PostgreSQL to 9.3, and some GBIF links.
web/.htaccess: mod_autoindex: show .* files which are normally hidden, because these are important parts of our codebase. (the leading . is not used for access controls.) .svn folders will remain hidden to avoid clutter.
web/links/index.htm: updated to Firefox bookmarks. added links related to PostgreSQL plain-text pkeys and the GBIF data use agreement (which is apparently much less restrictive than the LoA we signed, and would even allow the data to be public). vegetation data: placed links into subfolders by datasource.
web/links/index.htm: updated to Firefox bookmarks. added links for EER models, data management plans. put PostgreSQL before MySQL because we have found PostgreSQL to be a much more capable database system, even though it lacks some of MySQL's user-friendly features.
web/links/index.htm: updated to Firefox bookmarks. PostgreSQL: ALTER TABLE: added documentation about disabling of foreign key triggers, which is only possible by the superuser. note that marking a foreign key constraint as NOT VALID does not disable the trigger, so NOT VALID cannot be used for this purpose. this would be used to add fkeys from core VegBIEN tables to validation results tables such as the geoscrubbing results, without needing to import the validation results directly into core VegBIEN (which is time-consuming and currently must be done before input data is loaded, requiring a datasource reload to add geoscrubbing results).
web/links/index.htm: updated to Firefox bookmarks. sudo: added instructions to turn off incorrect password e-mails.
bugfix: web/people/Brad_Boyle/.htaccess: only forward requests for a term defined by Brad to the attribution/ subdir, so that Brad.vegpath.org shows a directory listing instead of forwarding right to the attribution doc
bugfix: web/people/Brad_Boyle/.htaccess: set %{ENV:innermost_dir} to Brad_Boyle
added web/people/Brad_Boyle/data_provenance/ (BIEN database entities related to data provenance and ownership.docx)
bugfix: web/people/Brad_Boyle/attribution/.htaccess: \-escape the %s so that they aren't treated as backreferences. set the [redirect] flag so that the downloaded file has the correct filename (BIEN 3 data use and attribution.docx instead of attribution).
bugfix: web/people/Brad_Boyle/attribution/.htaccess: use %20 instead of + because the Apache server apparently doesn't translate + to space correctly
bugfix: web/people/Brad_Boyle/attribution/.htaccess: link to the VegBIEN subdir in /exchange_schemas instead of the main /VegBIEN because there are actually two VegBIEN subdirs, and the main one instead points to /datasources/VegBIEN
added web/people/Brad_Boyle/ with attribution/ subdir for BIEN 3 data use and attribution.docx
web/links/index.htm: updated to Firefox bookmarks. added Java client- and server-side links. web: split into client- and server-side folders.
web/links/index.htm: updated to Firefox bookmarks. added PostgreSQL links.
web/.htaccess: mod_autoindex: IndexHeadInsert: use IndexStyleSheet for stylesheet link instead
bugfix: web/.htaccess: mod_autoindex: IndexOptions: use +HTMLTable to ensure that the contents are always displayed in an HTML table, even when a header file is provided with HeaderName (which turns off the default HTML table for some reason)
web/links/index.htm: updated to Firefox bookmarks. MySQL: added steps to add a user if you are not root but have sudo access.
fix: web/links/index.htm: PostgreSQL: vacuuming: moved info about autovacuum process being aborted to correct bookmark
web/links/index.htm: updated to Firefox bookmarks. PostgreSQL: added info on vacuuming and analyzing.
web/links/index.htm: updated to Firefox bookmarks. Gmvault: added steps to do full backup and to backup only new e-mails
web/links/index.htm: updated to Firefox bookmarks. Gmvault: added run instructions for Mac.
web/links/index.htm: updated to Firefox bookmarks. added link to Gmvault (Gmail backup), which wouldn't install for me on Mac (but that may be because I'm using 10.8, and Gmvault is for 10.7/10.6)
bugfix: web/.htaccess: auto-detect dotpath in query string: need to include the path ($0) in the replacement, to avoid reverting to the root dir. (mod_rewrite replacements are not like relative URLs, which would interpret ?... as being relative to the current path, not the root.)
bugfix: web/.htaccess: auto-detect dotpath in query string: added missing $ at end of regexp
bugfix: web/.htaccess: parse dotpath in query string: make dotpath replacement start with ./ instead of / (which would incorrectly create an absolute URL path). this bug only appears when there is a trailing /, because this causes the matched text to be empty instead of a filesystem path with leading /.
bugfix: web/.htaccess: parse dotpath in query string: redirect so REQUEST_URI is populated from REQUEST_FILENAME: need to use - instead of $0 as the redirect destination so that REQUEST_FILENAME is used instead of the empty REQUEST_URI (i.e. the redirect vars are left untouched)
bugfix: web/.htaccess: parse dotpath in query string: need to add trailing / if dotpath so that dest path is URL path, not filesystem path (when trailing / missing, matched path is filesystem path)
added web/servers/vegbiendev/db/my/, which forwards to MySQL instead of PostgreSQL
web/servers/vegbiendev/db/: moved PostgreSQL engine to separate pg/ subdir to allow for other engines
web/links/index.htm: updated to Firefox bookmarks. added link to Brian Enquist's fractals video on PBS NOVA.
web/links/index.htm: updated to Firefox bookmarks. moved Linux, Mac into Unix folder. added instructions to remove old Linux kernels, which fill up the /boot partition. added instructions to force sed to use raw binary mode instead of UTF-8 when UTF-8 is set in the environment. added methods of implementing DB disk space quotas in Postgres. added comparison on my Mac's CPU (2.66 GHz Intel Core i5) with vegbiendev's (2.44 GHz AMD Phenom X4). my Mac's seems to be much faster, so it might make sense to check that the Thor CPUs are faster than the Vis Lab computers' CPUs the next time it gets upgraded. (these diffs can be seen in WinMerge with Moved block detection on. see /README.TXT > WinMerge setup for details.)
web/links/index.htm: updated to Firefox bookmarks. removed dead favicons. PostgreSQL: added bookmarks about triggers.
web/links/index.htm: updated to Firefox bookmarks. grouped version control systems into new version control folder.
web/links/index.htm: updated to Firefox bookmarks. sorted NCEAS bookmarks to put homepage and support pages first.
*{.sh,run}: use simpler .rel() instead of `. "$(dirname "${BASH_SOURCE0}")"/...` for relative includes
lib/Firefox_bookmarks.reformat.csv: unescape HTML in page's description, such as links to more info. this is necessary to properly render the persistent shells link in the screen > scrollback folder description.
web/links/index.htm: updated to Firefox bookmarks. `screen`: scrollback: added link to our wiki page on persistent shells, which are a better way to support reconnecting.
web/links/index.htm: updated to Firefox bookmarks. added bookmarks about the `screen` command, especially how to access the scrollback. resorted several folders alphabetically.
web/links/index.htm: updated to Firefox bookmarks. some broken favicons have also been fixed, by reopening bookmark in Firefox. (this will only update a favicon if there is a newer version. to delete a favicon completely, use Firefox's SQLite Manager plugin.)
web/index.php: use XHTML DOCTYPE to match what's used by mod_autoindex. this requires some adjustments in spacing for XHTML's slightly different formatting
bugfix: web/.htaccess: need to do DirectoryIndex redirects before checking for existing file/dir, because a DirectoryIndexed dir is existing but still needs to be redirected to the index.* file
web/.htaccess: mod_autoindex: use the main.css stylesheet to match the look-and-feel of index.php
web/.htaccess: mod_autoindex: Note that some listed files are not web-accessible: use ' instead of " to avoid \-escaping embedded "
web/.htaccess: mod_autoindex: sort by description when provided, to allow setting a custom (non-alphabetical) sort order using AddDescription
web/.htaccess: mod_autoindex: added note that some listed files are not web-accessible. they will produce a "Forbidden" error when clicked.
bugfix: web/index.php: added space between the full directory index and the preceding content
web/index.php: moved the full directory index within the rest of the document body
web/index.php: include full directory index, since the URL patterns list is just a subset of the content available through vegpath.org
web/.htaccess: added mod_autoindex IndexOptions, in particular FoldersFirst
bugfix: web/.htaccess: changed "mod_dir listing"->"mod_autoindex listing" because mod_dir does not actually handle the autogenerated listings
bugfix: web/.htaccess: DirectoryIndex: use disabled instead of on because on is actually treated as a filename, and does not invoke mod_autoindex. the DirectoryIndex directive and the mod_dir module actually apply only to manual index files, not to autogenerated dir listings (which are handled by mod_autoindex).
web/index.php: removed no longer needed custom alias j.mp/vegpath# for when page reached through vegbiendev.nceas.ucsb.edu, because vegpath.org is a much more reliable domain than the previous path.vg, and a separate way to reach VegPath when path.vg is down is no longer needed
web/.htaccess: <dir>/all forces mod_dir listing: use simpler $mod_dir_listing env var instead of query string modification to indicate that an explicit mod_dir listing should be displayed. this causes /all to replace ?index=1 as the way to force a mod_dir listing. note that the %{ENV:...} test needs to use $REDIRECT_mod_dir_listing instead of $mod_dir_listing, because a redirect will occur between the /all rule and the index.* rule, causing all env vars to be prepended with REDIRECT_ .
web/.htaccess: <dir>/all forces mod_dir listing, as a simpler syntax than ?index=1
web/.htaccess: for dirs, redirect to index.*: allow requesting a mod_dir listing instead with ?index=1
web/.htaccess: handle DirectoryIndex redirects in a RewriteRule instead of with `DirectoryIndex index`, so that RewriteConds can be used to configure when index.* is used as the DirectoryIndex instead of a mod_dir listing
web/.htaccess: handle DirectoryIndex subrequests when there is no DirectoryIndex: moved comment about -F subrequest after line it applies to
web/.htaccess: RewriteRules: added standard [discardpath,noescape,qsappend] options where missing (these should be the default, but aren't)
web/links/index.htm: updated to Firefox bookmarks. Mountain Lion upgrade: added Python psycopg2, Python OrderedDict, X11.
web/links/index.htm: updated to Firefox bookmarks. sorted MySQL and PostgreSQL sections.
web/links/index.htm: updated to Firefox bookmarks
web/links/index.htm: Mac 10.8 Mountain Lion > PostgreSQL: appended tab to name to disambiguate it from the general PostgreSQL section
bugfix: web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name: also renamed the corresponding self-anchor hyperlinks
bugfix: web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name: need to replace all occurrences (using /g option to sed) to include both HTML anchors on the line
web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name
web/links/index.htm: removed no longer needed - at the beginning of every folder's description
web/links/index.htm: updated to Firefox bookmarks. upgrading Mac OS X to 10.8 Mountain Lion: put fixes subdirs in order.
web/links/index.htm: updated to Firefox bookmarks. upgrading Mac OS X to 10.8 Mountain Lion: added fixes for Apache ~/Sites dirs, Apache PHP
web/links/index.htm: updated to Firefox bookmarks. added bookmarks for upgrading Mac OS X to 10.8 Mountain Lion. (WARNING: DO NOT upgrade unless you are prepared to fix several programs broken by the upgrade: svn, PostgreSQL. instructions are in the corresponding bookmark subdirs. these programs will be COMPLETELY UNAVAILABLE until they are manually fixed!)
web/links/index.htm: updated to Firefox bookmarks. regenerating also removed extra <a name=...> tags that were added when running index.htm.run on an already-processed index.htm.
lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links' names: hyperlink the added anchors as clickable paragraph marks (like Redmine), which take you to the HTML anchor. this is analogous to the clickable folder names which take you to their anchors.
lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links' names, in addition to their URLs
lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links using the URL itself as the anchor. these can be used to link to the comments attached to a bookmark in the bookmarks page, rather than to the bookmark's destination.
web/links/index.htm.run: use the runscript-common $top_file, which is equivalent to $linked_file
