bugfix: /README.TXT: Installation: Check out svn: need to use trunk instead of root
*: use vegbiendev:/home/bien instead of /home/bien/svn
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 ../
merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
web/BIEN3: link to Redmine instead of directly to the wiki, since the Redmine/ dir should manage where BIEN3 default-redirects to
schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/
schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/
added schemas/VegBIEN/data_dictionary/create_bien3_viewFullOccurrence.txt from Brad
added schemas/VegBIEN/data_dictionary/schema_docum.pptx from Brian McGill
removed no longer needed inputs/VegBIEN/fs symlink. use web/.fs instead.
web/.fs: changed to point directly to the svn root, so that the VegBIEN dir does not contain any recursive symlinks
/README.TXT: Mac settings backup: to Dropbox: stop Dropbox beforehand to prevent Dropbox from trying to capture filesystem events while syncing
/README.TXT: Mac settings backup: exclude ~/Library/Thunderbird/Profiles/9oo8rcyn.default/global-messages-db.sqlite because this file does not sync (issue #907)
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.")
schemas/VegBIEN/VegBIEN data dictionary.xlsx: moved to schemas/VegBIEN/data_dictionary/
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: analytical_stem_view: approved by/to discuss: renamed to * (removing "approved by") because the participants in today's conference call indicated that they were happy with the definitions, and the issues raised before the call had been addressed
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added all tables used to create analytical_stem_view, not just those that Brian M listed. (Brian M generated his tables list from the analytical_stem_view columns rather than the joins, and renamed plot.** to plot, which is why his list ended up missing tables and in the wrong order.)
added exports/2014-6-12.Jeff_Ott.climatic_range_determinants.csv.run
schemas/vegbien.sql: added 2014-6-12.Jeff_Ott.climatic_range_determinants (wiki.vegpath.org/Data_requests)
web/username_prefix.php: deletion comments: require ... strikethrough on both () to avoid ambiguity when the deleted part starts or ends with -
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: resized columns to fit laptop screen
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added my and Brian McGill's notes from the data dictionary conference call
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added analytical_stem_view table definitions
removed schemas/vegbien.ERD.MySQL_Workbench_6.1.6.mwb, because vegbien.ERD.mwb is now targeted to the correct version of MySQL Workbench (and is more up-to-date)
schemas/public_.sql: analytical_stem_view: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added "to discuss" column requested by Martha. resized columns to avoid truncating the viewFullOccurrence term names.
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating definitions of terms
web/username_prefix.php: deletion comments: also support strikethrough syntax for clarity: (c_)x@url -> c_x@url
added schemas/DwC/hist symlink to history/ to help fit URLs in the 63-char limit
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
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating viewFullOccurrence->analytical_stem_view and analytical_stem_view->viewFullOccurrence mappings
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: use new deletion comments (with () ) to indicate portions of external terms whose semantic meaning does not apply to our usage
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
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: removed extra rows and columns so that they aren't included when copying and pasting
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added tab to store viewFullOccurrence->analytical_stem_view mapping
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added viewFullOccurrence column
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)
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added links to editable and clickable versions of the spreadsheet, to enable switching back and forth between them. populated more definitions and links.
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
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: populated some definitions from VegCore data dictionary where available
bugfix: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: restored "" that had been stripped out when the data was copied out and pasted back, due to a bug in Google spreadsheets. prepended : before initial " as a workaround to prevent the " getting stripped out again.
schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated
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
fix: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: restored "" that had been stripped out when the data was pasted in. set column widths to fit on a laptop screen.
added schemas/VegBIEN/VegBIEN data dictionary.xlsx
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)
schemas/public_.sql: analytical_stem_view: example terms from each source: added location in the VegBIEN core DB
schemas/public_.sql: analytical_stem_view: terms in normalized schemas: put the source name right next to the term name (instead of after the table name) so it's easy to find
schemas/public_.sql: analytical_stem_view: VegX terms: populated definitions
schemas/public_.sql: analytical_stem_view: VegX terms: referenced to the specific table/subpath that they are in
bugfix: schemas/public_.sql: analytical_stem_view: locationName: re-sourced to VegX because this is actually not a DwC term
schemas/public_.sql: analytical_stem_view: populated definitions of linked DwC terms from DwC data dictionary
schemas/public_.sql: analytical_stem_view: renamed terms to link URLs, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#data-dictionary-rename-terms-to-link-URLs
inputs/.TNRS/schema.sql: unsafe_taxon_names(): removed the name with "spp." now that this TNRS bug (https://pods.iplantcollaborative.org/jira/browse/TNRS-193) has been fixed
schemas/public_.sql: analytical_stem_view: populated links from unrenamed term names, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#data-dictionary-populate-links-from-unrenamed-term-names
fix: schemas/public_.sql: analytical_stem_view: links: removed = before them because the link is in fact one member in a list of definitions (the = would apply to all definitions, not just the link, and since it apply to all definitions, it's redundant because of course the comment is what the column equals)
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)
fix: schemas/public_.sql: analytical_stem_view: vegpath.org links: use ; instead of : between link and definition, because it makes more grammatical sense
schemas/public_.sql: analytical_stem_view: vegpath.org links: removed no longer needed // suffix
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
