bugfix: web/.phpPgAdmin/.htaccess: work around phpPgAdmin bug that causes page to be ignored when not logged in
web/.phpPgAdmin/.htaccess: extract path components 1st->last: documented that can't use subject param for this because that goes to the last selected tab, not the default (leftmost) tab
*{.sh,run}: runscript targets: use begin_target instead of echo_func so the target name is properly echoed. note that this requires using with_rm so that $rm is properly progagated to applicable invoked targets. (previously, $rm was progagated to all invoked targets. note that with_rm only works inside a runscript target that starts with begin_target.)
web/links/index.htm: updated to Firefox bookmarks: Firefox: added instructions for enabling security.password_lifetime and making all tabs load when the browser is opened
web/links/index.htm: updated to Firefox bookmarks: Google Drive: listed bugs that make it very difficult to use (the need to re-download all files when reconnecting a client to an account). added recommendation not to use it (unstable).
web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: query planner: documented how to prevent incorrect query plans (`SET enable_seqscan = off;`, etc.)
web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: query planner: documented that incorrect query plans are an ongoing bug in Postgres, because it does not support index hints and by default does not follow the join order. specifically, Postgres often does the following things in query plans which should normally never be done:...
web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: added description of join_collapse_limit config param (which should be turned off, although it is on by default). added links for using TIDs ("the fastest possible access to a single row").
web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: added links for troubleshooting autovacuuming (which can slow queries down significantly when it isn't happening for any tables)
lib/Firefox_bookmarks.reformat.csv: "page's description": changed to "page's own description" to clarify that this is a description provided by the page itself
web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: added links for error reporting levels and how to hide stack traces in psql. SQL: added links for recursive queries, which can be used to traverse hierarchical (parent-pointer) tables.
web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: difference between STABLE and IMMUTABLE: functions that depend on the search_path: clarified that the confusing effects of using IMMUTABLE for one of these functions are only noticeable if the function is called on only constant values in a PL/pgSQL function (in which case the wrong search_path (the one in effect at create time) will be used)
web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: added explanation of the difference between STABLE and IMMUTABLE, and common pitfalls in using IMMUTABLE when you should use STABLE. svn: added troubleshooting steps for running `svn upgrade` after the last Mac system update, which upgrades svn.
web/links/index.htm: updated to Firefox bookmarks: Roundtable: virtual collaboration: annotated the linked pages
web/links/index.htm: updated to Firefox bookmarks: Roundtable: added materials for virtual collaboration roundtable. Mac: added steps for customizing screen saver security settings beyond the options supported in the UI.
web/links/index.htm: updated to Firefox bookmarks: Unix: moved into OS folder. Windows: added steps to try for fixing Windows Update.
web/links/index.htm: updated to Firefox bookmarks: Redmine: added links to the REST API for exporting data. svn: added instructions for using svnsync to export a repository. PostgreSQL: removed duplicate pages that were linked for multiple versions of Postgres.
web/.phpPgAdmin/.htaccess: support linking to a function
web/.phpPgAdmin/.htaccess: support linking to the functions list
web/.phpPgAdmin/.htaccess: support linking to a view
web/.phpPgAdmin/.htaccess: allow linking directly to the views list of a schema
web/.phpPgAdmin/.htaccess: refactored to build the URL incrementally, extracting path components 1st->last, instead of handling each # of path components as a separate case (which was more rigid and created unnecessary duplication)
bugfix: web/.phpPgAdmin/.htaccess: path RewriteRules: need to go directly to the applicable tab, rather than going via redirect.php, because redirect.php will use the last selected tab, rather than the first tab for that section, leading to unexpected results when a non-default tab was previously selected
web/BIEN3: redirected to .wiki since the wiki homepage now contains the list of all BIEN3 components
web/links/index.htm: updated to Firefox bookmarks. Quick links: use bien3.vegpath.org to link to the main BIEN3 page
added web/BIEN3 symlink, with .bien3 case-insensitive alias
web/links/index.htm: updated to Firefox bookmarks: wake for network access: added link to pmset man page, which contains commands for setting "wake for network access" for all power sources. note that "automatic restart on power loss" also needs to be set for all power sources, because the computer will always be in UPS mode at the time of a power failure.
web/links/index.htm: updated to Firefox bookmarks: NCEAS: added link to phone list, which contains the Balboa Building maintenance numbers
web/links/index.htm: updated to Firefox bookmarks: svn: added steps to add a file containing (append to the path)
(append
web/links/index.htm: updated to Firefox bookmarks: `mysql`: added commands to get interactive formatting (including echoed queries) when inputting from a file, and to get raw formatting when inputting from the console. git: added equivalent to `svn update`.
web/links/index.htm: updated to Firefox bookmarks: OS X 10.9 Mavericks upgrade: added links for whether to upgrade (conclusion: don't, it breaks existing programs)
web/links/index.htm: updated to Firefox bookmarks. git: added instructions to migrate from svn.
web/links/index.htm: updated to Firefox bookmarks. added instructions for running `svn switch` after moving everything into /trunk/ (for us, use `svn switch --force https://code.nceas.ucsb.edu/code/projects/bien/trunk # runtime: <1 min`).
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 "
