Activity
From 05/25/2014 to 06/23/2014
06/20/2014
06/19/2014
- 04:13 PM Revision 13831: bugfix: web/.phpPgAdmin/.htaccess: : handlers: use `chain` to only run them when the RewriteRule they apply to is run
- 04:11 PM Revision 13830: web/.phpPgAdmin/.htaccess: schema : handler: removed `env=subject:schema` because that has already been set
- 04:08 PM Revision 13829: web/.phpPgAdmin/.htaccess: tables: added : suffix handler
- 04:06 PM Revision 13828: bugfix: web/.phpPgAdmin/.htaccess: view : match: moved to right after `view=` because it only applies to views, not functions
- 03:58 PM Revision 13827: web/.phpPgAdmin/.htaccess: schema: page: indicate by prefixing with : to avoid needing to explicitly list all possible pages
- 03:54 PM Revision 13826: web/.phpPgAdmin/.htaccess: table: action: indicate by prefixing with : to avoid needing to explicitly list all possible actions
- 11:13 AM Revision 13825: exports/2014-6-12.Jeff_Ott.climatic_range_determinants.csv.run: updated export_() runtime (35 min) and rowcount (23 million)
- 02:33 AM Revision 13824: fix: /README.TXT: Full database import: disk space: removed instructions to rerun the import if the disk space gets used up, because this is actually a bug and is *not* generally "fixed just by rerunning the import"
- 02:27 AM Revision 13823: schemas/util.sql: lat_long_in_new_world(): use function rather than operator+search_path to allow inlining, which enables util.new_world() to only be evaluated once
- 02:24 AM Revision 13822: bugfix: schemas/util.sql: operator @(postgis.geography, postgis.geography): must use wrapper function because st_coveredby() needs postgis to be in the search_path
- 01:57 AM Revision 13821: fix: lib/runscripts/extract.run: export_(): explicitly prevent files from becoming web-accessible, to protect against an incorrect umask in the calling process
- 01:45 AM Revision 13820: fix: schemas/util.sql: point(): hide benign "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" notices
06/18/2014
- 08:56 PM Revision 13819: schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: also include New World occurrences by coordinates, using new lat_long_in_new_world(). this modification (as requested by Jeff) will help reduce the false negatives filtered out by including only data with placenames.
- 08:52 PM Revision 13818: schemas/public_.sql: added lat_long_in_new_world() wrapper around util.lat_long_in_new_world()
- 08:49 PM Revision 13817: schemas/util.sql: lat_long_in_new_world(): documented that this includes false positives above and below the New World bounding box, as described in util.bounding_box()
- 08:44 PM Revision 13816: schemas/util.sql: bounding_box(): documented that the geography type stores all edges as arcs of great circles, resulting in the latitude lines bulging outward from the true bounding box. this will create false positives above and below the bounding box.
- 08:38 PM Revision 13815: schemas/util.sql: added lat_long_in_new_world()
- 08:35 PM Revision 13814: schemas/util.sql: added operator @(postgis.geography, postgis.geography). can't use && for this because it only compares 2D bounding boxes (which are geometry objects that do not support geocoordinate wraparound).
- 08:06 PM Revision 13813: schemas/util.sql: added point()
- 08:00 PM Revision 13812: schemas/util.sql: new_world(): removed no longer needed cast to postgis.geography
- 07:59 PM Revision 13811: bugfix: schemas/util.sql: bounding_box(): must use postgis.geography (instead of postgis.geometry) because that handles geocoordinate wraparound correctly
- 07:52 PM Revision 13810: bugfix: schemas/util.sql: bounding_box(): need to explicitly set SRID to make sure the correct value is used
- 07:39 PM Revision 13809: bugfix: schemas/util.sql: bounding_box(): use st_makeenvelope() instead of st_makebox2d() because st_makebox2d() doesn't support geocoordinate wraparound (it is not SRID-aware)
- 07:32 PM Revision 13808: schemas/util.sql: new_world(): removed no longer needed cast to postgis.geometry
- 07:31 PM Revision 13807: schemas/util.sql: bounding_box(): return postgis.geometry instead of postgis.box2d because box2d is not directly used in postgis functions
- 07:12 PM Revision 13806: bugfix: /Makefile: mk_db: plpython3u: use CREATE EXTENSION instead of createlang so that the plpython3u extension is created in addition to the plpython3u language (as it is on Linux)
- 04:43 PM Revision 13805: schemas/util.sql: added new_world()
- 04:30 PM Revision 13804: bugfix: schemas/util.sql: bounding_box(): use util.range instead of numrange to support wraparound ranges for geocoordinates
- 04:26 PM Revision 13803: schemas/util.sql: range(numeric, numeric): use util.range instead of numrange to support wraparound ranges (which use a modulus system such as geocoordinates)
- 04:20 PM Revision 13802: schemas/util.sql: added `range` type (and cast to numrange), which allows wraparound ranges such as for geocoordinates
- 03:56 PM Revision 13801: schemas/util.sql: bounding_box(): documented usage
- 03:53 PM Revision 13800: schemas/public_.sql, inputs/.TNRS/schema.sql: upgraded to Postgres 9.3.4 format, which removes trailing " "
- 03:52 PM Revision 13799: schemas/util.sql: added bounding_box()
- 03:41 PM Revision 13798: bugfix: /Makefile: postgis schema: also need to make it accessible to non-superusers
- 03:12 PM Revision 13797: /Makefile, /README.TXT: PostgreSQL: Mac OS X: switched to using homebrew, which supports PostGIS
- 01:40 PM Revision 13796: backups/TNRS.backup.md5: updated
06/17/2014
- 04:48 PM Revision 13795: schemas/util.sql: range(numeric, numeric): use simpler numrange() constructor instead of text input syntax
- 04:39 PM Revision 13794: schemas/util.sql: operator functions: renamed to plain-text names to follow the Postgres convention of making the function name be the human-readable name of the operator
- 04:26 PM Revision 13793: fix: bin/in_place: usage: removed duplicate copy of [preserve_mtime=1]
- 04:22 PM Revision 13792: /Makefile: removed no longer used nonApacheOnPort80 code
- 04:13 PM Revision 13791: bugfix: /Makefile: phppgadmin-Linux: don't change the Apache port if something "else" is running on port 80, because this feature was only needed when tomcat was running on that port, but is now buggy
06/16/2014
- 06:50 PM Revision 13790: schemas/util.sql: added ~ operator for ranges
- 04:35 PM Revision 13789: /Makefile: mk_db: added PostGIS so it can be used by our functions
- 04:34 PM Revision 13788: bugfix: /Makefile: postgres-Linux: postgis: updated apt-get target names for Ubuntu 14.04
- 03:52 PM Revision 13787: **/LICENSE.TXT: use lowercase when there is a single set of *__*
- 03:50 PM Revision 13786: /LICENSE.TXT: refers to: removed trunk/ because of course it also applies to the branches/ and tags/ subdirs
- 02:13 PM Revision 13785: schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: allow geovalid_bien = NULL to enable filtering New World status by coordinates rather than country
- 02:03 PM Revision 13784: schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: added geovalid_bien
06/13/2014
- 08:34 PM Revision 13783: web/util.js: removed no longer used parse_dot_path(), etc. this is handled by web/.htaccess instead.
- 08:24 PM Revision 13782: web/index.php: Brad: added attribution/
- 08:22 PM Revision 13781: web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.
- 08:21 PM Revision 13780: web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.
- 08:11 PM Revision 13779: web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs
- 08:11 PM Revision 13778: web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs
- 08:08 PM Revision 13777: added web/people/Brad_Boyle/identifiers
- 08:07 PM Revision 13776: bugfix: web/index.php: Brad: updated resource names to match filesystem
- 07:58 PM Revision 13775: bugfix: web/index.php: Brad: fixed URL base
- 07:57 PM Revision 13774: web/index.php: sources: reordered/recategorized to match the subdirs and wiki.vegpath.org/VegCore
- 07:56 PM Revision 13773: schemas/VegCore/.htaccess: RewriteBase: use full path
- 07:43 PM Revision 13772: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 07:08 PM Revision 13771: schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/
- 07:06 PM Revision 13770: added web/people/Brad_Boyle/identifier_examples, which is used by the VegBIEN data dictionary
- 07:02 PM Revision 13769: placed web/BIEN3/TWiki/lib/LocalSite.cfg under version control because it contains absolute paths that need to be maintained
- 07:01 PM Revision 13768: web/main.conf: updated paths
- 06:34 PM Revision 13767: web/people/Brad_Boyle/*/.htaccess: set the destination filename using RewriteRule env, to allow escaping " " with "\ " instead of the difficult-to-read "\%20"
- 06:20 PM Revision 13766: web/people/Brad_Boyle/*/.htaccess: use relative paths to new symlinks to avoid hardcoding paths
- 06:07 PM Revision 13765: web/BIEN3/TWiki/twiki.conf: updated paths
- 05:51 PM Revision 13764: bugfix: /README.TXT: Installation: Check out svn: need to use trunk instead of root
- 05:49 PM Revision 13763: *: use vegbiendev:/home/bien instead of /home/bien/svn
- 05:15 PM Revision 13762: web/people/Brad_Boyle/: added symlinks to Brad's files that are used in the data dictionaries
- 04:29 PM Revision 13761: schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/
- 04:11 PM Revision 13760: schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
- 04:09 PM Revision 13759: web/BIEN3/Redmine/svn/.htaccess: removed unneeded RewriteBase because this does not use a relative redirect with ../
- 04:07 PM Revision 13758: schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
- 04:02 PM Revision 13757: schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
- 04:01 PM Revision 13756: schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
- 03:58 PM Revision 13755: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 03:40 PM Revision 13754: web/BIEN3: link to Redmine instead of directly to the wiki, since the Redmine/ dir should manage where BIEN3 default-redirects to
- 03:26 PM Revision 13753: schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/
- 02:20 PM Revision 13752: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 02:20 PM Revision 13751: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 02:18 PM Revision 13750: schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/
- 02:10 PM Revision 13749: schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/
- 02:01 PM Revision 13748: added schemas/VegBIEN/data_dictionary/create_bien3_viewFullOccurrence.txt from Brad
- 01:58 PM Revision 13747: schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/
- 01:26 PM Revision 13746: added schemas/VegBIEN/data_dictionary/schema_docum.pptx from Brian McGill
- 01:16 PM Revision 13745: merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
- 01:03 PM Revision 13744: removed no longer needed inputs/VegBIEN/fs symlink. use web/.fs instead.
- 12:56 PM Revision 13743: web/.fs: changed to point directly to the svn root, so that the VegBIEN dir does not contain any recursive symlinks
- 10:51 AM Revision 13742: /README.TXT: Mac settings backup: to Dropbox: stop Dropbox beforehand to prevent Dropbox from trying to capture filesystem events while syncing
- 10:18 AM Revision 13741: /README.TXT: Mac settings backup: exclude ~/Library/Thunderbird/Profiles/9oo8rcyn.default/global-messages-db.sqlite because this file does not sync (issue #907)
- 08:45 AM Revision 13740: 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.`.
06/12/2014
- 08:03 PM Revision 13739: web/username_prefix.php: username/password prompt message: added instructions to always append "." when visiting the homepage of the site ("vegpath.org.")
- 07:10 PM Revision 13738: schemas/VegBIEN/VegBIEN data dictionary.xlsx: moved to schemas/VegBIEN/data_dictionary/
- 05:42 PM Revision 13737: 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
- 05:32 PM Revision 13736: 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.)
- 03:56 PM Revision 13735: added exports/2014-6-12.Jeff_Ott.climatic_range_determinants.csv.run
- 03:53 PM Revision 13734: schemas/vegbien.sql: added 2014-6-12.Jeff_Ott.climatic_range_determinants (wiki.vegpath.org/Data_requests)
- 03:38 PM Revision 13733: web/username_prefix.php: deletion comments: require -...- strikethrough on both () to avoid ambiguity when the deleted part starts or ends with -
- 11:51 AM Revision 13732: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: resized columns to fit laptop screen
- 10:43 AM Revision 13731: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added my and Brian McGill's notes from the data dictionary conference call
- 08:00 AM Revision 13730: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added analytical_stem_view table definitions
- 07:38 AM Revision 13729: 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)
06/10/2014
- 07:35 PM Revision 13728: 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
- 07:20 PM Revision 13727: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added "to discuss" column requested by Martha. resized columns to avoid truncating the viewFullOccurrence term names.
- 03:40 PM Revision 13726: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating definitions of terms
- 03:05 PM Revision 13725: web/username_prefix.php: deletion comments: also support strikethrough syntax for clarity: (-c_-)x@url -> c_x@url
- 02:30 PM Revision 13724: added schemas/DwC/hist symlink to history/ to help fit URLs in the 63-char limit
- 11:48 AM Revision 13723: 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
- 11:38 AM Revision 13722: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating viewFullOccurrence->analytical_stem_view and analytical_stem_view->viewFullOccurrence mappings
- 11:12 AM Revision 13721: 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
- 11:09 AM Revision 13720: 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.
- 10:59 AM Revision 13719: web/username_prefix.php: comments: use [] instead of () because in writing, [] denotes insertion, while () (as an editing mark) denotes something to remove
- 10:58 AM Revision 13718: web/username_prefix.php: comments: use [] instead of () because in writing, [] denotes insertion, while () (as an editing mark) denotes something to remove
- 10:15 AM Revision 13717: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: removed extra rows and columns so that they aren't included when copying and pasting
- 10:11 AM Revision 13716: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added tab to store viewFullOccurrence->analytical_stem_view mapping
- 09:55 AM Revision 13715: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added viewFullOccurrence column
06/09/2014
- 05:26 PM Revision 13714: 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)
- 04:19 PM Revision 13713: 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.
- 12:49 PM Revision 13712: web/username_prefix.php: word-wraps: renamed to linewraps
- 12:48 PM Revision 13711: 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)
- 12:12 PM Revision 13710: 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.
- 11:33 AM Revision 13709: web/username_prefix.php: comment prefixes: support embedded ":" in comment
06/07/2014
- 07:35 AM Revision 13708: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: populated some definitions from VegCore data dictionary where available
- 07:20 AM Revision 13707: 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.
- 07:15 AM Revision 13706: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated
- 07:04 AM Revision 13705: 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
- 12:22 AM Revision 13704: 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.
- 12:20 AM Revision 13703: 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.
- 12:12 AM Revision 13702: 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.
06/06/2014
- 11:52 PM Revision 13701: web/username_prefix.php: user2path(): visually separated steps for easier readability
- 11:30 PM Revision 13700: 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.
- 11:20 PM Revision 13699: added schemas/VegBIEN/VegBIEN data dictionary.xlsx
- 10:47 PM Revision 13698: 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 _
- 10:37 PM Revision 13697: 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 "."
- 10:34 PM Revision 13696: web/username_prefix.php: user2path(): padding used to visually separate 1st element of URL: support embedded @ inside highlighted part
- 10:18 PM Revision 13695: web/username_prefix.php: user2path(): added support for padding used to visually separate 1st element of URL (_x_@url -> x@url)
- 08:32 PM Revision 13694: bugfix: web/username_prefix.php: need to handle : in login (which would normally indicate a password)
- 08:43 AM Revision 13693: schemas/public_.sql: analytical_stem_view: example terms from each source: added location in the VegBIEN core DB
- 08:15 AM Revision 13692: 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
- 08:08 AM Revision 13691: schemas/public_.sql: analytical_stem_view: VegX terms: populated definitions
- 07:52 AM Revision 13690: schemas/public_.sql: analytical_stem_view: VegX terms: referenced to the specific table/subpath that they are in
- 07:32 AM Revision 13689: bugfix: schemas/public_.sql: analytical_stem_view: locationName: re-sourced to VegX because this is actually not a DwC term
- 07:24 AM Revision 13688: schemas/public_.sql: analytical_stem_view: populated definitions of linked DwC terms from DwC data dictionary
- 07:09 AM Revision 13687: 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
- 06:47 AM Revision 13686: 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
- 06:44 AM Revision 13685: 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
- 06:02 AM Revision 13684: 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)
- 05:27 AM Revision 13683: 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
- 05:24 AM Revision 13682: web/.htaccess: auto-detect dotpath: removed handling of no longer used @ prefix (used to be used by username-based prefix subpaths)
- 05:18 AM Revision 13681: bugfix: web/.htaccess: username-based prefix subpaths: usernames_disabled: also need to support it being set in the current round
- 05:16 AM Revision 13680: 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
- 05:07 AM Revision 13679: bugfix: web/.htaccess: forced mod_autoindex listing: use $usernames_disabled to ensure that usernames stay disabled even when /all path is removed
- 05:06 AM Revision 13678: 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)
- 05:01 AM Revision 13677: bugfix: web/.htaccess: username-based prefix subpaths: REDIRECT_REQUEST_URI: also allow it to be unset, as it is when using usernames
- 04:57 AM Revision 13676: fix: web/index.php: directory index: don't append QUERY_STRING, as this is not used by /all
- 04:57 AM Revision 13675: web/.htaccess: username-based prefix subpaths: removed usernames_disabled env var because the bug that appeared to require this has now been fixed
- 04:56 AM Revision 13674: 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
- 04:39 AM Revision 13673: web/.htaccess: username-based prefix subpaths: allow explicitly disabling in a RewriteRule to handle special cases
- 04:28 AM Revision 13672: web/.htaccess: auto-detect dotpath: removed handling of no longer used @ prefix (used to be used by username-based prefix subpaths)
- 04:20 AM Revision 13671: 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)
- 02:44 AM Revision 13670: fix: schemas/public_.sql: analytical_stem_view: vegpath.org links: use ; instead of : between link and definition, because it makes more grammatical sense
- 02:42 AM Revision 13669: schemas/public_.sql: analytical_stem_view: vegpath.org links: removed no longer needed // suffix
- 02:38 AM Revision 13668: 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.
- 02:19 AM Revision 13667: bugfix: web/.htaccess: subdomains: each path element must be non-empty, to avoid matching a trailing . incorrectly
- 01:18 AM Revision 13666: web/.htaccess: username-based prefix subpaths: updated documentation to use leading // instead of trailing ? or ?@
- 01:14 AM Revision 13665: web/username_prefix.php: $_SERVER["PHP_AUTH_USER"] test: factored $_SERVER["SCRIPT_URL"] out of both branches of if statement
- 12:36 AM Revision 13664: web/username_prefix.php: don't remove @ from query string because that is no longer a special character
- 12:08 AM Revision 13663: schemas/public_.sql: analytical_stem_view: added links and definitions for half a dozen of the terms from various sources
06/05/2014
- 11:46 PM Revision 13662: 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
- 08:38 PM Revision 13661: web/.phpPgAdmin/.htaccess: action redirect: only append ? if adding to the query string
- 01:17 PM Revision 13660: inputs/publishable datasources.xlsx: updated
- 01:17 PM Revision 13659: inputs/publishable datasources.xlsx: updated
- 12:27 PM Revision 13658: inputs/publishable datasources.xlsx: updated
- 12:12 PM Revision 13657: inputs/publishable datasources.xlsx: updated
- 11:33 AM Revision 13656: web/.phpPgAdmin/.htaccess: view: default to displaying the columns rather than the definition
- 09:02 AM Revision 13655: schemas/public_.sql: analytical_stem_view: indicated provenance of the rest of the terms
- 08:32 AM Revision 13654: schemas/public_.sql: analytical_stem_view: flagged the DwC terms
- 08:20 AM Revision 13653: web/.phpPgAdmin/.htaccess: support viewing the columns of a view rather than the definition
- 08:16 AM Revision 13652: web/.phpPgAdmin/.htaccess: RewriteRules: use overridable action var
- 08:14 AM Revision 13651: web/.phpPgAdmin/.htaccess: support overriding action param in a later RewriteRule
- 08:04 AM Revision 13650: web/.phpPgAdmin/.htaccess: removed skip= because this creates a confusing control flow, and prevents using chain
- 07:51 AM Revision 13649: backups/TNRS.backup.md5: updated
- 07:30 AM Revision 13648: schemas/public_.sql: added plot.**.modify()
- 07:24 AM Revision 13647: inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()
- 07:21 AM Revision 13646: inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()
- 07:15 AM Revision 13645: fix: schemas/util.sql: view_def_to_orig(): also need to merge .* expressions resulting from a SELECT * of a join, to avoid duplicated columns
- 06:52 AM Revision 13644: fix: schemas/util.sql: view_def_to_orig(): require at least 6 cols to avoid false positives in the expansion match pattern
- 06:49 AM Revision 13643: bugfix: schemas/util.sql: view_def_to_orig(): 1st col: can't prepend \y because it considers only \w chars, not "
- 06:35 AM Revision 13642: bugfix: schemas/util.sql: view_def_to_orig(): don't match whitespace in the middle of a "" identifier, as this could throw off the parser
- 06:34 AM Revision 13641: schemas/util.sql: eval(): restore user's intent by running util.view_def_to_orig() on the query to unexpand expanded * expressions
- 05:50 AM Revision 13640: schemas/util.sql: pg_get_viewdef(): use util.view_def_to_orig()
- 05:50 AM Revision 13639: schemas/util.sql: added view_def_to_orig()
- 05:46 AM Revision 13638: fix: schemas/util.sql: pg_get_viewdef(): should be STABLE because it references system catalogs
- 05:44 AM Revision 13637: schemas/util.sql: added pg_get_viewdef() wrapper, which unexpands expanded * expressions
- 04:30 AM Revision 13636: lib/tnrs.py: max_names: raised back up to 500 now that a workaround for the Internal Server Errors is in place (https://github.com/iPlantCollaborativeOpenSource/TNRS/issues/7)
- 03:57 AM Revision 13635: fix: schemas/public_.sql: tnrs_input_name: added ORDER BY to ensure a stable sort order. this also creates better query plans by enabling merge joins.
- 03:50 AM Revision 13634: bugfix: schemas/public_.sql: tnrs_input_name: need to exclude unsafe taxon names as a workaround to #935 (TNRS crashes when scrubbing names with two infraspecific epithets)
- 03:45 AM Revision 13633: schemas/public_.sql: taxonlabel: added index on taxonomicname to facilitate retrieving rows from tnrs_input_name
- 03:39 AM Revision 13632: inputs/.TNRS/schema.sql: added taxon_name_is_safe()
- 03:30 AM Revision 13631: inputs/.TNRS/schema.sql: added unsafe_taxon_names()
06/04/2014
- 03:01 PM Revision 13630: fix: lib/tnrs.py: max_names: lowered to 50 because the dev TNRS server is now always crashing with an Internal Server Error when scrubbing 500 names at a time (https://github.com/iPlantCollaborativeOpenSource/TNRS/issues/7)
- 11:41 AM Revision 13629: 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
- 11:14 AM Revision 13628: 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
- 02:25 AM Revision 13627: web/username_prefix.php: no prefix: use $_SERVER["SCRIPT_URL"] instead of rtrimming $_SERVER["REQUEST_URI"]
- 02:24 AM Revision 13626: web/username_prefix.php: has prefix: use same expr whether or not it has a query string, because the with-query-string expr works for both cases
- 02:20 AM Revision 13625: web/username_prefix.php: use if statements instead of `? :` for clarity
- 02:10 AM Revision 13624: web/username_prefix.php: use $subpath instead of $_SERVER["PHP_AUTH_USER"] for clarity
- 02:09 AM Revision 13623: bugfix: **/.htaccess: redirects with fragment: qsappend does not support fragment, so append it separately
- 01:59 AM Revision 13622: web/.htaccess, username_prefix.php: username-based prefix subpaths: support dotpath in query string (which will be appended verbatim to the prefix). use "__?@__" instead of "__?__&" to signal username-based prefix, so that the query string does not end in a dangling & .
- 01:53 AM Revision 13621: bugfix: inputs/.TNRS/.htaccess: qsappend does not support fragment, so append it separately
- 01:06 AM Revision 13620: bugfix: web/.htaccess: auto-detect dotpath in query string: don't exclude dotpaths that come before a normal query string (&k=v...)
- 01:05 AM Revision 13619: web/.htaccess: auto-detect dotpath in query string: documented what each RewriteCond does
- 01:03 AM Revision 13618: web/.htaccess: auto-detect dotpath in query string: use %{QUERY_STRING} instead of %0 for clarity
- 12:48 AM Revision 13617: web/.htaccess, web/username_prefix.php: username-based prefix subpaths: support query strings in addition to paths
- 12:18 AM Revision 13616: web/index.php: removed no longer needed redirection of username-based prefix subpaths, which is now handled by web/.htaccess
- 12:16 AM Revision 13615: web/.htaccess: handle username-based prefix subpaths (of the form "subpath@url?") for all paths rather than just for the root (which were handled by index.php)
- 12:11 AM Revision 13614: added web/username_prefix.php, for use with username-based prefix redirects
06/03/2014
- 11:13 PM Revision 13613: web/index.php: subpath@host? redirects: also support multiple @ and nested . in prefix: a@b.c@host? -> host?b.c.a
- 11:01 PM Revision 13612: web/index.php: support prefix redirect of the form subpath@host? , which is better than subpath.host because case is preserved and special chars allowed. (must require trailing ? for redirect, to avoid needing login to view the page itself.)
- 10:47 PM Revision 13611: bugfix: web/index.php: full directory index: appending query string: need to use $_SERVER["QUERY_STRING"], not $_SERVER["HTTP_AUTHORIZATION"] for this
- 11:36 AM Revision 13610: schemas/public_.sql: sync_*(): renamed to *_modify() to facilitate finding these functions when modifying the corresponding view (using the new naming convention for a view's on-modify function)
- 10:36 AM Revision 13609: bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields
- 10:25 AM Revision 13608: bugfix: schemas/util.sql: mk_drop_from_create(): need to match first rather than last CREATE
- 10:21 AM Revision 13607: inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this
- 09:52 AM Revision 13606: schemas/util.sql: recreate_view(): support omitting the view_query if the view has already been modified (eg. for public.*_view, which allow changing the view as a separate step)
- 08:56 AM Revision 13605: fix: schemas/public_.sql: sync_*(): use util.copy() instead of CREATE TABLE AS so that table and column comments are also copied. this avoids the need to separately add the same comments to the view *and* its materialized table.
- 08:52 AM Revision 13604: bugfix: schemas/util.sql: recreate(): need to handle case where util.mk_drop_from_create() is NULL
- 08:45 AM Revision 13603: bugfix: schemas/util.sql: mk_drop_from_create(): only match CREATE if no custom DROP came before it
- 08:29 AM Revision 13602: bugfix: schemas/public_.sql: sync_geoscrub_input_to_view(): `CREATE TABLE geoscrub_input AS __`: needs `LIMIT 0`
- 08:19 AM Revision 13601: fix: schemas/util.sql: explain2notice_msg_if_can(): also need to catch invalid_cursor_definition ("cannot open multi-query plan as cursor")
- 08:15 AM Revision 13600: schemas/public_.sql: sync_analytical_stem_to_view(): removed DROP TABLE IF EXISTS because this is now done automatically by util.recreate()
- 07:39 AM Revision 13599: schemas/util.sql: added copy()
- 07:36 AM Revision 13598: schemas/util.sql: added copy_data()
06/02/2014
- 04:24 PM Revision 13597: fix: lib/tnrs.py: Constrain by Source: turn it on so that the download settings reflect what TNRS actually used, while this is broken
- 06:19 AM Revision 13596: fix: lib/tnrs.py: max_names: reduced back to 500 because even 5000 crashes the dev TNRS server
- 05:52 AM Revision 13595: lib/tnrs.py: max_names: reduced to 5000 because 100,000 causes an internal server error
- 05:25 AM Revision 13594: bugfix: /README.TXT: Full database import: To run TNRS: to rescrub all names: also need to re-create public-schema views that were cascadingly deleted
- 05:23 AM Revision 13593: /README.TXT: Full database import: To run TNRS: added steps to rescrub all names
- 04:59 AM Revision 13592: backups/TNRS.backup.md5: updated
- 04:50 AM Revision 13591: lib/tnrs.py: switched to downloading all matches per name, as is needed to implement #917. note that this will break the parts of the schema that use the tnrs table, until Brad's match-picking algorithm can be implemented, but this tradeoff is necessary to be able to begin scrubbing sooner (Martha; wiki.vegpath.org/2014-05-29_conference_call#TNRS)
- 04:35 AM Revision 13590: schemas/vegbien.sql: tnrs_input_name: don't scrub accepted names, as using multiple matches per name no longer provides a single accepted name to scrub. instead, the Accepted_* fields can be whitespace-split to generate the same columns that would have been generated by the scrubbing (and without the overhead of the extra TNRS call).
- 04:27 AM Revision 13589: fix: inputs/.TNRS/schema.sql: added back index on Name_submitted, which is needed for tnrs_input_name to work properly (now that there is no automatic index created by a unique constraint)
- 04:08 AM Revision 13588: schemas/vegbien.sql: tnrs_input_name: don't scrub accepted names, as using multiple matches per name no longer provides a single accepted name to scrub. instead, the Accepted_* fields can be whitespace-split to generate the same columns that would have been generated by the scrubbing (and without the overhead of the extra TNRS call).
- 03:43 AM Revision 13587: fix: inputs/.TNRS/schema.sql: tnrs: removed unique constraint on Name_submitted, Name_matched because there can be more than one match with the same Name_matched (but different accepted names, etc.)
06/01/2014
- 09:00 PM Revision 13586: fix: inputs/.TNRS/schema.sql: tnrs.tnrs__valid_match index: made it non-unique to allow multiple matches per name, as is needed to implement #917
- 05:00 AM Revision 13585: bugfix: inputs/.TNRS/schema.sql: tnrs__match_num__fill(): only fill if not set, to support case where tnrs is being restored from a .sql file (where match_num is already set)
- 04:36 AM Revision 13584: inputs/.TNRS/schema.sql: tnrs: documented runtime to add a constraint (3 min)
- 04:35 AM Revision 13583: inputs/.TNRS/schema.sql: unique constraint on Name_submitted: added Name_matched to allow multiple matches per name, as is needed to implement #917
- 03:44 AM Revision 13582: inputs/.TNRS/schema.sql: tnrs: documented how to populate a new column
- 03:41 AM Revision 13581: inputs/.TNRS/schema.sql: tnrs: pkey: use match_num instead of Name_number to allow multiple matches per name, as is needed to implement #917
05/31/2014
- 10:31 PM Revision 13580: inputs/.TNRS/schema.sql: tnrs.match_num: made it NOT NULL now that it's populated
- 10:28 PM Revision 13579: inputs/.TNRS/schema.sql: tnrs: populate match_num
- 10:25 PM Revision 13578: inputs/.TNRS/schema.sql: tnrs: populate match_num
- 09:50 PM Revision 13577: inputs/.TNRS/schema.sql: tnrs: documented how to add and remove columns
- 08:58 PM Revision 13576: inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line
- 08:58 PM Revision 13575: inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line
- 08:11 PM Revision 13574: inputs/test_taxonomic_names/_scrub/*: updated to TNRS schema
- 08:10 PM Revision 13573: inputs/.TNRS/schema.sql: tnrs: added match_num
- 08:06 PM Revision 13572: inputs/.TNRS/data.sql.run: refresh(): documented runtime (1 min)
- 08:03 PM Revision 13571: schemas/Makefile: added back rename/%, which *is* used by `inputs/.TNRS/data.sql.run refresh`. updated it to use schema bundles.
- 06:44 PM Revision 13570: inputs/.TNRS/schema.sql: added tnrs__match_num__next()
- 06:29 PM Revision 13569: inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)
- 05:06 AM Revision 13568: exports/2014-3-11.Jeff_Ott.climatic_range_determinants.csv.run: documented export_() runtime (11 min) and rowcount (11 million matching the filter criteria)
05/30/2014
- 06:34 PM Revision 13567: inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)
- 06:22 PM Revision 13566: schemas/util.sql: added seq__reset()
- 06:15 PM Revision 13565: schemas/util.sql: added seq__create()
- 06:11 PM Revision 13564: fix: schemas/util.sql: try_cast(), is_castable(): also catch invalid_schema_name, thrown by `'pg_temp.__'::regclass`
- 02:49 PM Revision 13563: backups/TNRS.backup.md5: updated
- 07:50 AM Revision 13562: lib/tnrs.py: max_names: increased to 100000 because the dev server can handle more names (no simultaneous users), as decided in the conference call (wiki.vegpath.org/2014-05-29_conference_call#TNRS)
- 07:42 AM Revision 13561: schemas/vegbien.ERD.mwb: regenerated exports
- 07:39 AM Revision 13560: schemas/vegbien.ERD.mwb: re-updated to schemas/vegbien.my.sql, which now recognizes the broken tables. fixed sync issues. vegbien.ERD.mwb is now fully in sync with vegbien.my.sql.
- 07:37 AM Revision 13559: fix: lib/PostgreSQL-MySQL.csv: need to replace "double precision" with "double" to work with MySQL Workbench 5.2.47
- 06:58 AM Revision 13558: schemas/vegbien.ERD.mwb: updated to schemas/vegbien.my.sql. some tables weren't recognized (likely due to bugs in MySQL Workbench 5.2.47), and have been left as-is (unsynced). note that downgrading to 5.2.35 is not an option, because that is fatally broken by a system upgrade.
- 05:58 AM Revision 13557: fix: schemas/vegbien.ERD.mwb: use schemas/vegbien.my.sql instead of schemas/vegbien.my.sql.changes.sql as the sync source
- 05:27 AM Revision 13556: schemas/vegbien.ERD.mwb: switched back to MySQL Workbench 6.1.6 version, which also works with MySQL Workbench 5.2.47
- 05:17 AM Revision 13555: schemas/vegbien.ERD.mwb: restored version for MySQL Workbench 5.2.35 (undid r13549), as 6.1.6 has bugs in the DDL file sync
- 05:05 AM Revision 13554: schemas/vegbien.ERD.mwb: renamed to vegbien.ERD.MySQL_Workbench_6.1.6.mwb to differentiate the versions for different versions of MySQL Workbench
- 04:49 AM Revision 13553: removed no longer used config/VirtualBox_VMs/VegCore ERD/. use the Ubuntu 14.04 VM instead, which now has the VegCore ERD setup.
- 04:48 AM Revision 13552: config/VirtualBox_VMs/Ubuntu 14.04/Ubuntu 14.04.vbox: added VegCore ERD setup
- 03:30 AM Revision 13551: schemas/: svn:ignore *.changes.sql, needed for MySQL Workbench 6.1.6
- 03:30 AM Revision 13550: schemas/vegbien.ERD.mwb: updated
- 03:16 AM Revision 13549: schemas/vegbien.ERD.mwb: updated layout for MySQL Workbench 6.1.6, which uses a different line spacing
05/29/2014
- 11:53 AM Revision 13548: lib/tnrs.py: commented out the value of max_names that is not active, for clarity
05/28/2014
- 03:54 PM Revision 13547: config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated: merged post-bootloader installation steps into one snapshot now that eth1 addition is successful
- 03:49 PM Revision 13546: config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated, which adds eth1
- 03:47 PM Revision 13545: config/VirtualBox_VMs/Ubuntu 12.04/Ubuntu 12.04.vbox: updated
05/27/2014
- 11:12 PM Revision 13544: lib/tnrs.py: sources: updated to list/sort order in issue #917
- 10:39 PM Revision 13543: added exports/2014-3-11.Jeff_Ott.climatic_range_determinants.csv.run
- 10:38 PM Revision 13542: schemas/public_.sql: added 2014-3-11.Jeff_Ott.climatic_range_determinants
- 10:17 PM Revision 13541: schemas/public_.sql: analytical_stem_view: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
- 10:13 PM Revision 13540: inputs/.TNRS/schema.sql: taxon_scrub.scrubbed_unique_taxon_name.*: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
- 10:09 PM Revision 13539: schemas/public_.sql: added scrubbed_specific_epithet, scrubbed_species_binomial, which are needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
- 10:08 PM Revision 13538: fix: schemas/public_.sql: sync_analytical_stem_to_view(): removed fkey to source.shortname because this prevents reloading individual datasources
- 09:19 PM Revision 13537: added downloads/
- 03:27 AM Revision 13536: schemas/public_.sql: added scrubbed_specific_epithet, scrubbed_species_binomial, which are needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
- 03:21 AM Revision 13535: fix: schemas/util.sql: mk_drop_from_create(): also support CREATE queries that include the SELECT statement on the same line as the CREATE
- 12:33 AM Revision 13534: schemas/public_.sql: analytical_stem_view: scrubbed_morphospecies_binomial: use new taxon_scrub.scrubbed_morphospecies_binomial
- 12:28 AM Revision 13533: inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*
- 12:13 AM Revision 13532: inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*
05/26/2014
- 11:54 PM Revision 13531: inputs/.TNRS/schema.sql: taxon_scrub: documented how to modify it
- 11:51 PM Revision 13530: inputs/.TNRS/schema.sql: added taxon_scrub_modify()
- 11:41 PM Revision 13529: schemas/util.sql: create_if_not_exists(): print message if already exists, so the function doesn't inexplicably appear not to have run at all
- 11:20 PM Revision 13528: inputs/.TNRS/schema.sql: added taxon_scrub_modify()
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