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From 05/20/2014 to 06/18/2014

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.
Aaron Marcuse-Kubitza
08:52 PM Revision 13818: schemas/public_.sql: added lat_long_in_new_world() wrapper around util.lat_long_in_new_world()
Aaron Marcuse-Kubitza
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()
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
08:38 PM Revision 13815: schemas/util.sql: added lat_long_in_new_world()
Aaron Marcuse-Kubitza
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).
Aaron Marcuse-Kubitza
08:06 PM Revision 13813: schemas/util.sql: added point()
Aaron Marcuse-Kubitza
08:00 PM Revision 13812: schemas/util.sql: new_world(): removed no longer needed cast to postgis.geography
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:52 PM Revision 13810: bugfix: schemas/util.sql: bounding_box(): need to explicitly set SRID to make sure the correct value is used
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
07:32 PM Revision 13808: schemas/util.sql: new_world(): removed no longer needed cast to postgis.geometry
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
04:43 PM Revision 13805: schemas/util.sql: added new_world()
Aaron Marcuse-Kubitza
04:30 PM Revision 13804: bugfix: schemas/util.sql: bounding_box(): use util.range instead of numrange to support wraparound ranges for geocoordinates
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
04:20 PM Revision 13802: schemas/util.sql: added `range` type (and cast to numrange), which allows wraparound ranges such as for geocoordinates
Aaron Marcuse-Kubitza
03:56 PM Revision 13801: schemas/util.sql: bounding_box(): documented usage
Aaron Marcuse-Kubitza
03:53 PM Revision 13800: schemas/public_.sql, inputs/.TNRS/schema.sql: upgraded to Postgres 9.3.4 format, which removes trailing " "
Aaron Marcuse-Kubitza
03:52 PM Revision 13799: schemas/util.sql: added bounding_box()
Aaron Marcuse-Kubitza
03:41 PM Revision 13798: bugfix: /Makefile: postgis schema: also need to make it accessible to non-superusers
Aaron Marcuse-Kubitza
03:12 PM Revision 13797: /Makefile, /README.TXT: PostgreSQL: Mac OS X: switched to using homebrew, which supports PostGIS
Aaron Marcuse-Kubitza
01:53 PM Task #917: TNRS: Instructions for new version with TPL
all the taxon names have now been rescrubbed Aaron Marcuse-Kubitza
01:40 PM Revision 13796: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza

06/17/2014

05:25 PM Task #935 (Resolved): TNRS crashes when scrubbing names with two infraspecific epithets
iPlant fixed this Aaron Marcuse-Kubitza
04:48 PM Revision 13795: schemas/util.sql: range(numeric, numeric): use simpler numrange() constructor instead of text input syntax
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
04:26 PM Revision 13793: fix: bin/in_place: usage: removed duplicate copy of [preserve_mtime=1]
Aaron Marcuse-Kubitza
04:22 PM Revision 13792: /Makefile: removed no longer used nonApacheOnPort80 code
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza

06/16/2014

06:50 PM Revision 13790: schemas/util.sql: added ~ operator for ranges
Aaron Marcuse-Kubitza
04:35 PM Revision 13789: /Makefile: mk_db: added PostGIS so it can be used by our functions
Aaron Marcuse-Kubitza
04:34 PM Revision 13788: bugfix: /Makefile: postgres-Linux: postgis: updated apt-get target names for Ubuntu 14.04
Aaron Marcuse-Kubitza
03:52 PM Revision 13787: **/LICENSE.TXT: use lowercase when there is a single set of *__*
Aaron Marcuse-Kubitza
03:50 PM Revision 13786: /LICENSE.TXT: refers to: removed trunk/ because of course it also applies to the branches/ and tags/ subdirs
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
02:03 PM Revision 13784: schemas/public_.sql: 2014-6-12.Jeff_Ott.climatic_range_determinants: added geovalid_bien
Aaron Marcuse-Kubitza

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.
Aaron Marcuse-Kubitza
08:24 PM Revision 13782: web/index.php: Brad: added attribution/
Aaron Marcuse-Kubitza
08:22 PM Revision 13781: web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.
Aaron Marcuse-Kubitza
08:21 PM Revision 13780: web/index.php: removed no longer used PHP redirects. these are now handled by Apache .htaccess files instead.
Aaron Marcuse-Kubitza
08:11 PM Revision 13779: web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs
Aaron Marcuse-Kubitza
08:11 PM Revision 13778: web/people/Brad_Boyle/data_provenance: abbreviated to provenance to enable shorter URLs
Aaron Marcuse-Kubitza
08:08 PM Revision 13777: added web/people/Brad_Boyle/identifiers
Aaron Marcuse-Kubitza
08:07 PM Revision 13776: bugfix: web/index.php: Brad: updated resource names to match filesystem
Aaron Marcuse-Kubitza
07:58 PM Revision 13775: bugfix: web/index.php: Brad: fixed URL base
Aaron Marcuse-Kubitza
07:57 PM Revision 13774: web/index.php: sources: reordered/recategorized to match the subdirs and wiki.vegpath.org/VegCore
Aaron Marcuse-Kubitza
07:56 PM Revision 13773: schemas/VegCore/.htaccess: RewriteBase: use full path
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:08 PM Revision 13771: schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/
Aaron Marcuse-Kubitza
07:06 PM Revision 13770: added web/people/Brad_Boyle/identifier_examples, which is used by the VegBIEN data dictionary
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:01 PM Revision 13768: web/main.conf: updated paths
Aaron Marcuse-Kubitza
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"
Aaron Marcuse-Kubitza
06:20 PM Revision 13766: web/people/Brad_Boyle/*/.htaccess: use relative paths to new symlinks to avoid hardcoding paths
Aaron Marcuse-Kubitza
06:07 PM Revision 13765: web/BIEN3/TWiki/twiki.conf: updated paths
Aaron Marcuse-Kubitza
05:51 PM Revision 13764: bugfix: /README.TXT: Installation: Check out svn: need to use trunk instead of root
Aaron Marcuse-Kubitza
05:49 PM Revision 13763: *: use vegbiendev:/home/bien instead of /home/bien/svn
Aaron Marcuse-Kubitza
05:15 PM Revision 13762: web/people/Brad_Boyle/: added symlinks to Brad's files that are used in the data dictionaries
Aaron Marcuse-Kubitza
04:29 PM Revision 13761: schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
04:09 PM Revision 13759: web/BIEN3/Redmine/svn/.htaccess: removed unneeded RewriteBase because this does not use a relative redirect with ../
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
03:26 PM Revision 13753: schemas/VegBIEN/taxonomy/: moved into schemas/VegBIEN/planning/
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
02:18 PM Revision 13750: schemas/VegBIEN/attribution/: moved into schemas/VegBIEN/planning/
Aaron Marcuse-Kubitza
02:10 PM Revision 13749: schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/
Aaron Marcuse-Kubitza
02:01 PM Revision 13748: added schemas/VegBIEN/data_dictionary/create_bien3_viewFullOccurrence.txt from Brad
Aaron Marcuse-Kubitza
01:58 PM Revision 13747: schemas/VegBIEN/growth_forms/: moved into schemas/VegBIEN/planning/
Aaron Marcuse-Kubitza
01:26 PM Revision 13746: added schemas/VegBIEN/data_dictionary/schema_docum.pptx from Brian McGill
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
01:03 PM Revision 13744: removed no longer needed inputs/VegBIEN/fs symlink. use web/.fs instead.
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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.`.
Aaron Marcuse-Kubitza

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.")
Aaron Marcuse-Kubitza
07:10 PM Revision 13738: schemas/VegBIEN/VegBIEN data dictionary.xlsx: moved to schemas/VegBIEN/data_dictionary/
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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.)
Aaron Marcuse-Kubitza
03:56 PM Revision 13735: added exports/2014-6-12.Jeff_Ott.climatic_range_determinants.csv.run
Aaron Marcuse-Kubitza
03:53 PM Revision 13734: schemas/vegbien.sql: added 2014-6-12.Jeff_Ott.climatic_range_determinants (wiki.vegpath.org/Data_requests)
Aaron Marcuse-Kubitza
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 -
Aaron Marcuse-Kubitza
11:51 AM Revision 13732: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: resized columns to fit laptop screen
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
10:11 AM Task #937 (New): fix missing date fields
* -do a search for null date fields to figure out which datasources this applies to- _see "missing dates spreadsheet"... Aaron Marcuse-Kubitza
08:00 AM Revision 13730: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added analytical_stem_view table definitions
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza

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
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
03:40 PM Revision 13726: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating definitions of terms
Aaron Marcuse-Kubitza
03:05 PM Revision 13725: web/username_prefix.php: deletion comments: also support strikethrough syntax for clarity: (-c_-)x@url -> c_x@url
Aaron Marcuse-Kubitza
02:30 PM Revision 13724: added schemas/DwC/hist symlink to history/ to help fit URLs in the 63-char limit
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
11:38 AM Revision 13722: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: finished populating viewFullOccurrence->analytical_stem_view and analytical_stem_view->viewFullOccurrence mappings
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
10:11 AM Revision 13716: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added tab to store viewFullOccurrence->analytical_stem_view mapping
Aaron Marcuse-Kubitza
09:55 AM Revision 13715: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: added viewFullOccurrence column
Aaron Marcuse-Kubitza

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)
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
12:49 PM Revision 13712: web/username_prefix.php: word-wraps: renamed to linewraps
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
11:33 AM Revision 13709: web/username_prefix.php: comment prefixes: support embedded ":" in comment
Aaron Marcuse-Kubitza

06/07/2014

07:35 AM Revision 13708: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated: populated some definitions from VegCore data dictionary where available
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
07:15 AM Revision 13706: schemas/VegBIEN/VegBIEN data dictionary.xlsx: updated
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza

06/06/2014

11:52 PM Revision 13701: web/username_prefix.php: user2path(): visually separated steps for easier readability
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
11:20 PM Revision 13699: added schemas/VegBIEN/VegBIEN data dictionary.xlsx
Aaron Marcuse-Kubitza
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 _
Aaron Marcuse-Kubitza
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 "."
Aaron Marcuse-Kubitza
10:34 PM Revision 13696: web/username_prefix.php: user2path(): padding used to visually separate 1st element of URL: support embedded @ inside highlighted part
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
08:32 PM Revision 13694: bugfix: web/username_prefix.php: need to handle : in login (which would normally indicate a password)
Aaron Marcuse-Kubitza
08:45 AM Task #934: Data Dictionary
added links where link creation could be automated, and populated the example terms from each source Aaron Marcuse-Kubitza
08:43 AM Revision 13693: schemas/public_.sql: analytical_stem_view: example terms from each source: added location in the VegBIEN core DB
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
08:08 AM Revision 13691: schemas/public_.sql: analytical_stem_view: VegX terms: populated definitions
Aaron Marcuse-Kubitza
07:52 AM Revision 13690: schemas/public_.sql: analytical_stem_view: VegX terms: referenced to the specific table/subpath that they are in
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:24 AM Revision 13688: schemas/public_.sql: analytical_stem_view: populated definitions of linked DwC terms from DwC data dictionary
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
04:57 AM Revision 13676: fix: web/index.php: directory index: don't append QUERY_STRING, as this is not used by /all
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
04:39 AM Revision 13673: web/.htaccess: username-based prefix subpaths: allow explicitly disabling in a RewriteRule to handle special cases
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
02:42 AM Revision 13669: schemas/public_.sql: analytical_stem_view: vegpath.org links: removed no longer needed // suffix
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
02:19 AM Revision 13667: bugfix: web/.htaccess: subdomains: each path element must be non-empty, to avoid matching a trailing . incorrectly
Aaron Marcuse-Kubitza
01:18 AM Revision 13666: web/.htaccess: username-based prefix subpaths: updated documentation to use leading // instead of trailing ? or ?@
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
12:36 AM Revision 13664: web/username_prefix.php: don't remove @ from query string because that is no longer a special character
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza

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
Aaron Marcuse-Kubitza
08:38 PM Revision 13661: web/.phpPgAdmin/.htaccess: action redirect: only append ? if adding to the query string
Aaron Marcuse-Kubitza
01:17 PM Revision 13660: inputs/publishable datasources.xlsx: updated
Aaron Marcuse-Kubitza
01:17 PM Revision 13659: inputs/publishable datasources.xlsx: updated
Aaron Marcuse-Kubitza
12:27 PM Revision 13658: inputs/publishable datasources.xlsx: updated
Aaron Marcuse-Kubitza
12:12 PM Revision 13657: inputs/publishable datasources.xlsx: updated
Aaron Marcuse-Kubitza
11:33 AM Revision 13656: web/.phpPgAdmin/.htaccess: view: default to displaying the columns rather than the definition
Aaron Marcuse-Kubitza
09:04 AM Task #934: Data Dictionary
indicated provenance of the @analytical_stem_view@ (viewFullOccurrence) terms Aaron Marcuse-Kubitza
09:02 AM Revision 13655: schemas/public_.sql: analytical_stem_view: indicated provenance of the rest of the terms
Aaron Marcuse-Kubitza
08:32 AM Revision 13654: schemas/public_.sql: analytical_stem_view: flagged the DwC terms
Aaron Marcuse-Kubitza
08:20 AM Revision 13653: web/.phpPgAdmin/.htaccess: support viewing the columns of a view rather than the definition
Aaron Marcuse-Kubitza
08:16 AM Revision 13652: web/.phpPgAdmin/.htaccess: RewriteRules: use overridable action var
Aaron Marcuse-Kubitza
08:14 AM Revision 13651: web/.phpPgAdmin/.htaccess: support overriding action param in a later RewriteRule
Aaron Marcuse-Kubitza
08:04 AM Revision 13650: web/.phpPgAdmin/.htaccess: removed skip= because this creates a confusing control flow, and prevents using chain
Aaron Marcuse-Kubitza
07:51 AM Revision 13649: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
07:30 AM Revision 13648: schemas/public_.sql: added plot.**.modify()
Aaron Marcuse-Kubitza
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()
Aaron Marcuse-Kubitza
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()
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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 "
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
05:50 AM Revision 13640: schemas/util.sql: pg_get_viewdef(): use util.view_def_to_orig()
Aaron Marcuse-Kubitza
05:50 AM Revision 13639: schemas/util.sql: added view_def_to_orig()
Aaron Marcuse-Kubitza
05:46 AM Revision 13638: fix: schemas/util.sql: pg_get_viewdef(): should be STABLE because it references system catalogs
Aaron Marcuse-Kubitza
05:44 AM Revision 13637: schemas/util.sql: added pg_get_viewdef() wrapper, which unexpands expanded * expressions
Aaron Marcuse-Kubitza
04:42 AM Task #936 (New): in TNRS client, detect Internal Server Errors when they occur instead of after the pauses have timed out
the problem is that an "is it ready" check can produce a variety of errors, including Internal Server Errors, but all... Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
03:53 AM Task #935: TNRS crashes when scrubbing names with two infraspecific epithets
a workaround has been implemented that filters out unsafe taxon names. however, the unsafe names are hardcoded, so a ... Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
03:45 AM Revision 13633: schemas/public_.sql: taxonlabel: added index on taxonomicname to facilitate retrieving rows from tnrs_input_name
Aaron Marcuse-Kubitza
03:39 AM Revision 13632: inputs/.TNRS/schema.sql: added taxon_name_is_safe()
Aaron Marcuse-Kubitza
03:30 AM Revision 13631: inputs/.TNRS/schema.sql: added unsafe_taxon_names()
Aaron Marcuse-Kubitza

06/04/2014

10:23 PM Task #935 (Resolved): TNRS crashes when scrubbing names with two infraspecific epithets
h3. problem
the error occurs on this name:
Lamiaceae Agastache pallidiflora (Heller) Rydb. spp. pallidiflora va...
Aaron Marcuse-Kubitza
06:00 PM Task #917: TNRS: Instructions for new version with TPL
The taxon names Brad sent for testing the rescrubbing are now attached. Martha Narro
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)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
02:25 AM Revision 13627: web/username_prefix.php: no prefix: use $_SERVER["SCRIPT_URL"] instead of rtrimming $_SERVER["REQUEST_URI"]
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
02:20 AM Revision 13625: web/username_prefix.php: use if statements instead of `? :` for clarity
Aaron Marcuse-Kubitza
02:10 AM Revision 13624: web/username_prefix.php: use $subpath instead of $_SERVER["PHP_AUTH_USER"] for clarity
Aaron Marcuse-Kubitza
02:09 AM Revision 13623: bugfix: **/.htaccess: redirects with fragment: qsappend does not support fragment, so append it separately
Aaron Marcuse-Kubitza
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 & .
Aaron Marcuse-Kubitza
01:53 AM Revision 13621: bugfix: inputs/.TNRS/.htaccess: qsappend does not support fragment, so append it separately
Aaron Marcuse-Kubitza
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...)
Aaron Marcuse-Kubitza
01:05 AM Revision 13619: web/.htaccess: auto-detect dotpath in query string: documented what each RewriteCond does
Aaron Marcuse-Kubitza
01:03 AM Revision 13618: web/.htaccess: auto-detect dotpath in query string: use %{QUERY_STRING} instead of %0 for clarity
Aaron Marcuse-Kubitza
12:48 AM Revision 13617: web/.htaccess, web/username_prefix.php: username-based prefix subpaths: support query strings in addition to paths
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
12:11 AM Revision 13614: added web/username_prefix.php, for use with username-based prefix redirects
Aaron Marcuse-Kubitza

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
Aaron Marcuse-Kubitza
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.)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
03:24 PM Task #934 (New): Data Dictionary
Define the Data Dictionary terms for VegBIEN and associated tables.
# -First define the (approximately 60) terms nee...
Martha Narro
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)
Aaron Marcuse-Kubitza
10:36 AM Revision 13609: bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields
Aaron Marcuse-Kubitza
10:25 AM Revision 13608: bugfix: schemas/util.sql: mk_drop_from_create(): need to match first rather than last CREATE
Aaron Marcuse-Kubitza
10:21 AM Revision 13607: inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
08:52 AM Revision 13604: bugfix: schemas/util.sql: recreate(): need to handle case where util.mk_drop_from_create() is NULL
Aaron Marcuse-Kubitza
08:45 AM Revision 13603: bugfix: schemas/util.sql: mk_drop_from_create(): only match CREATE if no custom DROP came before it
Aaron Marcuse-Kubitza
08:29 AM Revision 13602: bugfix: schemas/public_.sql: sync_geoscrub_input_to_view(): `CREATE TABLE geoscrub_input AS __`: needs `LIMIT 0`
Aaron Marcuse-Kubitza
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")
Aaron Marcuse-Kubitza
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()
Aaron Marcuse-Kubitza
07:39 AM Revision 13599: schemas/util.sql: added copy()
Aaron Marcuse-Kubitza
07:36 AM Revision 13598: schemas/util.sql: added copy_data()
Aaron Marcuse-Kubitza

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
Aaron Marcuse-Kubitza
06:19 AM Revision 13596: fix: lib/tnrs.py: max_names: reduced back to 500 because even 5000 crashes the dev TNRS server
Aaron Marcuse-Kubitza
05:52 AM Revision 13595: lib/tnrs.py: max_names: reduced to 5000 because 100,000 causes an internal server error
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
05:23 AM Revision 13593: /README.TXT: Full database import: To run TNRS: added steps to rescrub all names
Aaron Marcuse-Kubitza
04:59 AM Revision 13592: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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).
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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).
Aaron Marcuse-Kubitza
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.)
Aaron Marcuse-Kubitza

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
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
04:36 AM Revision 13584: inputs/.TNRS/schema.sql: tnrs: documented runtime to add a constraint (3 min)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
03:44 AM Revision 13582: inputs/.TNRS/schema.sql: tnrs: documented how to populate a new column
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza

05/31/2014

10:31 PM Revision 13580: inputs/.TNRS/schema.sql: tnrs.match_num: made it NOT NULL now that it's populated
Aaron Marcuse-Kubitza
10:28 PM Revision 13579: inputs/.TNRS/schema.sql: tnrs: populate match_num
Aaron Marcuse-Kubitza
10:25 PM Revision 13578: inputs/.TNRS/schema.sql: tnrs: populate match_num
Aaron Marcuse-Kubitza
09:50 PM Revision 13577: inputs/.TNRS/schema.sql: tnrs: documented how to add and remove columns
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
08:11 PM Revision 13574: inputs/test_taxonomic_names/_scrub/*: updated to TNRS schema
Aaron Marcuse-Kubitza
08:10 PM Revision 13573: inputs/.TNRS/schema.sql: tnrs: added match_num
Aaron Marcuse-Kubitza
08:06 PM Revision 13572: inputs/.TNRS/data.sql.run: refresh(): documented runtime (1 min)
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
06:44 PM Revision 13570: inputs/.TNRS/schema.sql: added tnrs__match_num__next()
Aaron Marcuse-Kubitza
06:29 PM Revision 13569: inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza

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)
Aaron Marcuse-Kubitza
06:22 PM Revision 13566: schemas/util.sql: added seq__reset()
Aaron Marcuse-Kubitza
06:15 PM Revision 13565: schemas/util.sql: added seq__create()
Aaron Marcuse-Kubitza
06:11 PM Revision 13564: fix: schemas/util.sql: try_cast(), is_castable(): also catch invalid_schema_name, thrown by `'pg_temp.__'::regclass`
Aaron Marcuse-Kubitza
02:49 PM Revision 13563: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
07:42 AM Revision 13561: schemas/vegbien.ERD.mwb: regenerated exports
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
04:48 AM Revision 13552: config/VirtualBox_VMs/Ubuntu 14.04/Ubuntu 14.04.vbox: added VegCore ERD setup
Aaron Marcuse-Kubitza
03:30 AM Revision 13551: schemas/: svn:ignore *.changes.sql, needed for MySQL Workbench 6.1.6
Aaron Marcuse-Kubitza
03:30 AM Revision 13550: schemas/vegbien.ERD.mwb: updated
Aaron Marcuse-Kubitza
03:16 AM Revision 13549: schemas/vegbien.ERD.mwb: updated layout for MySQL Workbench 6.1.6, which uses a different line spacing
Aaron Marcuse-Kubitza

05/29/2014

11:53 AM Revision 13548: lib/tnrs.py: commented out the value of max_names that is not active, for clarity
Aaron Marcuse-Kubitza

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
Aaron Marcuse-Kubitza
03:49 PM Revision 13546: config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated, which adds eth1
Aaron Marcuse-Kubitza
03:47 PM Revision 13545: config/VirtualBox_VMs/Ubuntu 12.04/Ubuntu 12.04.vbox: updated
Aaron Marcuse-Kubitza

05/27/2014

11:12 PM Revision 13544: lib/tnrs.py: sources: updated to list/sort order in issue #917
Aaron Marcuse-Kubitza
10:39 PM Revision 13543: added exports/2014-3-11.Jeff_Ott.climatic_range_determinants.csv.run
Aaron Marcuse-Kubitza
10:38 PM Revision 13542: schemas/public_.sql: added 2014-3-11.Jeff_Ott.climatic_range_determinants
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
09:24 PM Task #927 (Resolved): move morphospecies name formation to normalized DB
see [[TNRS derived columns#scrubbed_morphospecies_binomial]] > @scrubbed_morphospecies_binomial@ Aaron Marcuse-Kubitza
09:19 PM Revision 13537: added downloads/
Aaron Marcuse-Kubitza
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)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
12:33 AM Revision 13534: schemas/public_.sql: analytical_stem_view: scrubbed_morphospecies_binomial: use new taxon_scrub.scrubbed_morphospecies_binomial
Aaron Marcuse-Kubitza
12:28 AM Revision 13533: inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*
Aaron Marcuse-Kubitza
12:13 AM Revision 13532: inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*
Aaron Marcuse-Kubitza

05/26/2014

11:54 PM Revision 13531: inputs/.TNRS/schema.sql: taxon_scrub: documented how to modify it
Aaron Marcuse-Kubitza
11:51 PM Revision 13530: inputs/.TNRS/schema.sql: added taxon_scrub_modify()
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
11:20 PM Revision 13528: inputs/.TNRS/schema.sql: added taxon_scrub_modify()
Aaron Marcuse-Kubitza

05/23/2014

06:17 PM Revision 13527: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): use simpler util.recreate_view()
Aaron Marcuse-Kubitza
06:15 PM Revision 13526: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): documented usage
Aaron Marcuse-Kubitza
06:09 PM Revision 13525: schemas/util.sql: added recreate_view(), a special case of util.recreate()
Aaron Marcuse-Kubitza
04:24 PM Revision 13524: fix: schemas/util.sql: recreate(): usage: use `schema` instead of `schemas`
Aaron Marcuse-Kubitza
04:20 PM Revision 13523: config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated
Aaron Marcuse-Kubitza
03:57 PM Revision 13522: bugfix: schemas/public_.sql: _plots_20_tnrs_names: verbatim_name_with_author: use taxonverbatim.taxonomicname rather than taxonlabel.taxonomicname
Aaron Marcuse-Kubitza
02:16 AM Revision 13521: config/VirtualBox_VMs/Ubuntu */*.vbox: updated
Aaron Marcuse-Kubitza

05/22/2014

04:43 PM Task #932 (New): Discovering BIEN data through iPlant

iPlant will assign DOIs to datasets made public through its infrastructure. For the BIEN db data, the plan is:
* t...
Martha Narro
04:32 PM Task #931 (New): BIEN db at iPlant
Parent issue for tasks related to moving BIEN3 relational database and associated analytical views to iPlant. Martha Narro
04:20 PM Revision 13520: bugfix: config/VirtualBox_VMs/: switched from symlinks to hard links, because svn does not follow symlinks
Aaron Marcuse-Kubitza
02:07 PM Revision 13519: added config/VirtualBox_VMs/, containing the .vbox settings and password.txt (a non-empty password is needed for some system commands)
Aaron Marcuse-Kubitza

05/21/2014

07:30 PM Revision 13518: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): removed no longer needed DROP VIEW statement
Aaron Marcuse-Kubitza
07:30 PM Revision 13517: schemas/util.sql: recreate(): perform the correct DROP VIEW in the function itself so that the caller does not have to worry about forming it properly
Aaron Marcuse-Kubitza
07:19 PM Revision 13516: bugfix: schemas/util.sql: mk_drop_from_create(): added `DROP`
Aaron Marcuse-Kubitza
07:18 PM Revision 13515: schemas/util.sql: added mk_drop_from_create()
Aaron Marcuse-Kubitza
06:52 PM Revision 13514: schemas/util.sql: added regexp_match()
Aaron Marcuse-Kubitza
05:58 PM Revision 13513: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
05:50 PM Revision 13512: fix: schemas/util.sql: force_recreate(): renamed to just recreate(), because "force" normally implies that things will be deleted, which this function does not do
Aaron Marcuse-Kubitza
05:49 PM Revision 13511: fix: schemas/public_.sql: _plots_20_tnrs_names: fixed order of tnrs_taxonomic_status, tnrs_accepted_name_family
Aaron Marcuse-Kubitza
04:45 PM Revision 13510: schemas/public_.sql: _plots_20_tnrs_names: added tnrs_taxonomic_status, as requested in issue #915
Aaron Marcuse-Kubitza
04:34 PM Revision 13509: schemas/public_.sql: analytical_stem_view: taxonomic_status: don't filter with map_taxonomic_status() anymore since this is now done by "TNRS"."MatchedTaxon"
Aaron Marcuse-Kubitza
04:25 PM Revision 13508: fix: inputs/.TNRS/schema.sql: MatchedTaxon.taxonomicStatus: filter using map_taxonomic_status() so that the corrected value is available in the normalized DB, not just analytical_stem
Aaron Marcuse-Kubitza
04:05 PM Revision 13507: inputs/.TNRS/schema.sql: MatchedTaxon: to modify: use new MatchedTaxon_modify(), which eliminates the work of putting together the dependent views
Aaron Marcuse-Kubitza
03:53 PM Revision 13506: inputs/.TNRS/schema.sql: added MatchedTaxon_modify()
Aaron Marcuse-Kubitza
03:44 PM Revision 13505: schemas/util.sql: show_create_view(): use new mk_set_relation_metadata()
Aaron Marcuse-Kubitza
03:41 PM Revision 13504: schemas/util.sql: added mk_set_relation_metadata()
Aaron Marcuse-Kubitza
04:13 AM Revision 13503: bugfix: inputs/.TNRS/schema.sql: map_taxonomic_status(): need to use accepted name instead of scrubbed name (which also includes no-opinion names), as described at http://wiki.vegpath.org/2013-11-14_conference_call#taxonomic-fields. this used to be the accepted name, but got switched when the concatenated name was also used to store the matched name for no-opinion names.
Aaron Marcuse-Kubitza
01:50 AM Revision 13502: schemas/public_.sql: _plots_20_tnrs_names: use accepted_morphospecies_binomial, which is now available directly in the TNRS results, instead of just the morphospecies_suffix, as requested in issue #915
Aaron Marcuse-Kubitza
01:27 AM Revision 13501: inputs/.TNRS/schema.sql: MatchedTaxon: documented how to modify it (using util.force_recreate())
Aaron Marcuse-Kubitza
01:23 AM Revision 13500: fix: lib/PostgreSQL-MySQL.csv: also remove left-behind lines such as `$$);`
Aaron Marcuse-Kubitza
12:59 AM Revision 13499: schemas/util.sql: force_recreate(): documented usage, which is somewhat complex and has several important parts
Aaron Marcuse-Kubitza

05/20/2014

05:46 PM Revision 13498: inputs/.TNRS/schema.sql: MatchedTaxon, etc.: added accepted_morphospecies_binomial derived field
Aaron Marcuse-Kubitza
05:40 PM Revision 13497: bugfix: schemas/util.sql: restore_views(): need to specify view name for a manual existence check, in case the view definition becomes invalid, which would produce a nonstandard (uncatchable) exception
Aaron Marcuse-Kubitza
05:33 PM Revision 13496: bugfix: schemas/util.sql: explain(): don't display any log messages printed by IMMUTABLE functions in the query, which EXPLAIN apparently runs
Aaron Marcuse-Kubitza
05:21 PM Revision 13495: schemas/util.sql: create_if_not_exists(): added relation param, which can be used to ensure that a standard exception is always generated if the relation exists, even if the table definition would be invalid (which generates a variety of exceptions)
Aaron Marcuse-Kubitza
04:26 PM Task #929 (New): change TNRS client to store metadata
* see details in [[2013-06-13 conference call#include-TNRS-version-and-settings-in-TNRS-cache]]
* after implementi...
Aaron Marcuse-Kubitza
04:17 PM Task #928 (New): switch to new TNRS setup
# #927 (part of #915)
# #917
# #916 (using rescrubbed names)
# #915
# -#929 (metadata)- _postponed_
Aaron Marcuse-Kubitza
03:26 PM Task #927 (Resolved): move morphospecies name formation to normalized DB
* currently, it's only in the analytical_stem view Aaron Marcuse-Kubitza
02:39 PM Revision 13494: /README.TXT: to back up the vegbiendev databases: added step to review diff before performing backup, in case the backup scripts break and try to synchronize things incorrectly
Aaron Marcuse-Kubitza
 

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