Project

General

Profile

Statistics
| Revision:

# Date Author Comment
6359 11/21/2012 11:05 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Concatenated taxonlabel: Don't prepend family if the taxonName/scientificName itself is the family, so that the family is not duplicated in the concatenated taxonomic name

6358 11/21/2012 10:19 PM Aaron Marcuse-Kubitza

schemas/functions.sql: _nullIf(): Removed NOT NULL constraint on null param, to support use a (nullable) column rather than a literal as the null-equivalent value

6357 11/21/2012 09:08 PM Aaron Marcuse-Kubitza

xml_func.py: Simplifying functions: Added _nullIf(), to remove calls with no null value

6356 11/21/2012 09:00 PM Aaron Marcuse-Kubitza

xml_dom.py: Added prune_parent()

6355 11/21/2012 08:51 PM Aaron Marcuse-Kubitza

schemas/functions.sql: Added _or()

6354 11/21/2012 08:20 PM Aaron Marcuse-Kubitza

schemas/functions.sql: Added _merge_words()

6353 11/21/2012 08:04 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_*: Renamed geosourceValid to geovalid. (It had gotten renamed in the reference -> source rename.)

6352 11/21/2012 08:00 PM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Renamed georeferenceValid to geovalid

6351 11/21/2012 07:48 PM Aaron Marcuse-Kubitza

inputs/import.stats.xls: Updated import times. This now includes the Canadensys plants-related datasources HIBG, JBM, QFA, TRT, TRTE, UBC, VASCAN, and WIN.

6350 11/20/2012 09:59 PM Aaron Marcuse-Kubitza

inputs/import.stats.xls: Updated import times

6349 11/20/2012 09:42 PM Aaron Marcuse-Kubitza

Added inputs/HIBG/

6348 11/20/2012 09:33 PM Aaron Marcuse-Kubitza

Added inputs/JBM/

6347 11/20/2012 09:29 PM Aaron Marcuse-Kubitza

Added inputs/VASCAN/

6346 11/20/2012 09:22 PM Aaron Marcuse-Kubitza

Added inputs/WIN/

6345 11/20/2012 09:18 PM Aaron Marcuse-Kubitza

Added inputs/UBC/

6344 11/20/2012 09:14 PM Aaron Marcuse-Kubitza

Added inputs/TRTE/Specimen/

6343 11/20/2012 09:11 PM Aaron Marcuse-Kubitza

Added inputs/QFA/

6342 11/20/2012 09:06 PM Aaron Marcuse-Kubitza

Added inputs/TRT/

6341 11/20/2012 08:21 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Allow bien_read to SELECT from all tables in the public schema

6340 11/20/2012 08:10 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Allow bien_read to SELECT from analytical_aggregate, analytical_stem

6339 11/20/2012 08:09 PM Aaron Marcuse-Kubitza

lib/PostgreSQL-MySQL.csv: Removed GRANT/REVOKE because SCHEMA GRANTs are not supported in MySQL

6338 11/20/2012 07:57 PM Aaron Marcuse-Kubitza

pg_dump_vegbien: non-$owners mode: Removed --no-privileges in order to include GRANTs to other users

6337 11/20/2012 07:49 PM Aaron Marcuse-Kubitza

root Makefile: PostgreSQL: $(postgresReload-Linux): Making schemas/*.conf world-readable: Fixed bug where need to do this as the bien user, which owns the files

6336 11/20/2012 07:46 PM Aaron Marcuse-Kubitza

root Makefile: PostgreSQL: $(postgresReload-*): Make schemas/*.conf world-readable so it's readable by the postgres user, which the .conf installation is run as

6335 11/20/2012 07:43 PM Aaron Marcuse-Kubitza

root Makefile: PostgreSQL: $(postgresReload-*): Also install pg_hba.conf

6334 11/20/2012 07:36 PM Aaron Marcuse-Kubitza

root Makefile: PostgreSQL: Added postgres_reload to reload postgresql.conf and restart the DB

6333 11/20/2012 07:30 PM Aaron Marcuse-Kubitza

root Makefile: PostgreSQL: postgres-*: Factored postgresql.conf installation out in to $(postgresReload-*)

6332 11/20/2012 07:15 PM Aaron Marcuse-Kubitza

schemas/: Synced pg_hba.conf and pg_hba.Mac.conf's bien entries, which adds phpPgAdmin support (template1 access) on the Mac and bien_read access on Linux

6331 11/20/2012 06:56 PM Aaron Marcuse-Kubitza

root Makefile: VegBIEN DB: DB and users: Also create bien_read user for read-only access to the DB

6330 11/20/2012 06:53 PM Aaron Marcuse-Kubitza

schemas/pg_hba.Mac.conf: Allow access to the bien group rather than just the bien user, which will include bien_read

6329 11/20/2012 06:35 PM Aaron Marcuse-Kubitza

schemas/pg_hba.Mac.conf: Fixed bug where also need to allow password-based logins from the same machine, in order to work with pgAdmin

6328 11/20/2012 06:06 PM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.poster.pdf: Updated to 33x51in poster size and 0.25in margins

6327 11/20/2012 05:35 PM Aaron Marcuse-Kubitza

README.TXT: Schema changes: Creating a poster of the ERD: Added section with the State St FedEx Kinkos' rates for posters ($10.25/sq ft laminated)

6326 11/20/2012 05:29 PM Aaron Marcuse-Kubitza

README.TXT: Schema changes: Creating a poster of the ERD: Changed "Measure the fractional height of the text onscreen" to "Determine the poster size"

6325 11/20/2012 05:19 PM Aaron Marcuse-Kubitza

Added schemas/vegbien.ERD.poster.pdf

6324 11/20/2012 04:10 PM Aaron Marcuse-Kubitza

Added schemas/vegbien.ERD.poster.core.print_options.png

6323 11/20/2012 04:01 PM Aaron Marcuse-Kubitza

Added schemas/vegbien.ERD.poster.core.pdf

6322 11/20/2012 03:29 PM Aaron Marcuse-Kubitza

schemas/pg_hba.Mac.conf: Fixed bug where needed ident entry for postgres superuser

6321 11/20/2012 03:18 PM Aaron Marcuse-Kubitza

Added config/bien_read_password

6320 11/20/2012 02:53 PM Aaron Marcuse-Kubitza

README.TXT: Schema changes: Added instructions to calculate the minimum VegBIEN poster size (to make the text as least as big as on the VegBank ERD poster), which is 35x54in portrait

6319 11/19/2012 08:01 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: cultivated: Use location.iscultivated when taxonoccurrence.iscultivated is not available

6318 11/19/2012 07:55 PM Aaron Marcuse-Kubitza

Added inputs/FIA/FIA_COND_unique/, which contains the oldgrowth flag

6317 11/19/2012 07:53 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped oldGrowth

6316 11/19/2012 07:48 PM Aaron Marcuse-Kubitza

schemas/functions.sql: Added _not()

6315 11/19/2012 07:43 PM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Added oldGrowth

6314 11/19/2012 07:36 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot

6313 11/19/2012 07:35 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot

6312 11/19/2012 07:25 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: location: Added iscultivated for cases when entire plots rather than individual taxonoccurrences are marked as cultivated

6311 11/19/2012 07:17 PM Aaron Marcuse-Kubitza

inputs/FIA/: Added FIA_COND table from nimoy.geoscrub and code to generate a unique plot table from it, including the oldgrowth calculated field

6310 11/19/2012 06:46 PM Aaron Marcuse-Kubitza

Added inputs/FIA/Organism/postprocess.sql to cast PlotCD to a bigint

6309 11/19/2012 06:22 PM Aaron Marcuse-Kubitza

my2pg: Also remove (#) after bigint

6308 11/19/2012 06:05 PM Aaron Marcuse-Kubitza

Regenerated vegbien.ERD exports

6307 11/19/2012 06:03 PM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: Fixed lines

6306 11/19/2012 05:54 PM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: Fixed lines

6305 11/19/2012 05:54 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: source: Renamed fulltext to citation because according to the VegBank data dictionary <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=reference&entity=dba_tabledescription&where=where_tablename#fulltext> this is actually the full text of the reference citation, not of the reference itself (it would be unusual to store that in VegBank)

6304 11/19/2012 05:48 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Removed no longer needed sourcejournal, which can be stored in source and pointed to via parent_id instead of sourcejournal_id. sourcejournal.journal maps to source.fulltext, issn to isbn, and abbreviation to shortname.

6303 11/19/2012 05:48 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place

6302 11/19/2012 05:41 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: source: Added matched_source_id

6301 11/19/2012 05:34 PM Aaron Marcuse-Kubitza

sql.py: parse_exception(): function MissingCastException: If 1st param is hstore, only perform the cast on the value param. This fixes a bug in _map() calls whose value is a non-text type, such as SALVIAS.plotMetadata.AccessCode.

6300 11/19/2012 05:32 PM Aaron Marcuse-Kubitza

sql_io.py: cast(): Use sql_gen.Cast() to generate the cast, in order to take advantage of its support for casts to unknown

6299 11/19/2012 05:30 PM Aaron Marcuse-Kubitza

sql_gen.py: Cast: Support casts to unknown by casting to text first

6298 11/19/2012 04:59 PM Aaron Marcuse-Kubitza

schemas/postgresql.conf: Turn on the error log

6297 11/19/2012 04:58 PM Aaron Marcuse-Kubitza

schemas/pg_hba.conf: Also grant the bien user access to template1, which is accessed by phpPgAdmin

6296 11/19/2012 04:24 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: source: Added parent_id for nested sources, e.g. an article in a journal

6295 11/19/2012 04:23 PM Aaron Marcuse-Kubitza

lib/forwarding.Makefile: $(subdirs): Also exclude .archive/

6294 11/19/2012 04:09 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place

6293 11/19/2012 04:08 PM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: Fixed lines

6292 11/19/2012 03:54 PM Aaron Marcuse-Kubitza

Renamed inputs/_archive/ to .archive/ so it wouldn't be treated as a datasource

6291 11/19/2012 03:49 PM Aaron Marcuse-Kubitza

README.TXT: Documentation: Redmine-formatted list of steps for column-based import: Use ACAD instead of QMOR, which was removed

6290 11/19/2012 03:45 PM Aaron Marcuse-Kubitza

inputs/Makefile: Import logs: $(rsyncLogs): Include log files at any depth in the directory tree rather than just 1-2 levels deep. This adds log files whose containing directories have been moved to _archive/ directories.

6289 11/19/2012 03:29 PM Aaron Marcuse-Kubitza

Added inputs/_archive/

6288 11/19/2012 03:27 PM Aaron Marcuse-Kubitza

Removed inputs/QMOR/ because it's an insect collection

6287 11/19/2012 03:25 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: projectcontributor: Removed surname, since this information is stored in party_id->party.surname

6286 11/19/2012 03:23 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: projectcontributor: Removed cheatrole, since there is already a role field and this field was unused in VegBank

6285 11/19/2012 03:21 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: role: Added values from projectcontributor.ROLE_ID <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=projectcontributor&entity=dba_tabledescription&where=where_tablename#ROLE_ID>

6284 11/19/2012 03:17 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: sourcecontributor: role: Changed type to role

6283 11/19/2012 03:15 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: role enum: Added VegBank data dictionary values from <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1331&entity=dba_fielddescription&params=1331>

6282 11/19/2012 03:03 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: sourcecontributor: Renamed position to order for consistency with the ERD definition <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=referencecontributor&entity=dba_tabledescription&where=where_tablename#position> and disambiguation from other meanings of position which are similar to role

6281 11/19/2012 03:00 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: sourcecontributor: Renamed roletype to role for consistency with the ERD definition <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=referencecontributor&entity=dba_tabledescription&where=where_tablename#roleType>

6280 11/19/2012 02:53 PM Aaron Marcuse-Kubitza

inputs/.geoscrub/geoscrub_output/map.csv: Mapped to county, acceptedCounty

6279 11/19/2012 02:52 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place

6278 11/19/2012 02:50 PM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Added acceptedCounty

6277 11/19/2012 02:42 PM Aaron Marcuse-Kubitza

schemas/pg_hba.Mac.conf: Changed to match schemas/pg_hba.conf

6276 11/19/2012 02:37 PM Aaron Marcuse-Kubitza

schemas/pg_hba.conf: Fixed bug where also need an IPv6 bien entry with md5 authentication, because the IPv4 md5 authentication does not apply to "localhost", which is translated to the IPv6 address ::1

6275 11/19/2012 02:27 PM Aaron Marcuse-Kubitza

schemas/pg_hba.conf: Fixed bug where also need a local bien entry with md5 authentication, because the host-based md5 authentication applies only to literal IP addresses, not "localhost"

6274 11/19/2012 02:08 PM Aaron Marcuse-Kubitza

Added schemas/pg_hba.Mac.conf

6273 11/19/2012 02:01 PM Aaron Marcuse-Kubitza

schemas/pg_hba.conf: Restrict all accesses to the server except the bien user accessing vegbien using ident or a password, and the postgres superuser logging in using ident

6272 11/19/2012 01:25 PM Aaron Marcuse-Kubitza

inputs/.geoscrub/geoscrub_output/map.csv: Mapped countyvalidity to latLongInCounty

6271 11/19/2012 01:24 PM Aaron Marcuse-Kubitza

schemas/functions.sql: _map(): Fixed bug where entries that map to NULL were incorrectly being treated as if the entry didn't exist. Note that -> returns NULL both if the entry's value is NULL and if the entry doesn't exist, so ? must be used to recheck the presence of the key in the hstore.

6270 11/19/2012 12:48 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped latLongInCounty

6269 11/19/2012 12:46 PM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Added latLongInCounty

6268 11/19/2012 12:43 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added distance_to_county_m. Note that this can also be used to store latLongInCounty by mapping true to 0 and false to -1.

6267 11/19/2012 12:22 PM Aaron Marcuse-Kubitza

schemas/pg_hba.conf: Changed trust authentication back to ident/md5. Not sure how it got set to trust since I used md5 when enabling remote access to the DB for the bien user.

6266 11/19/2012 12:08 PM Aaron Marcuse-Kubitza

Added schemas/pg_hba.conf

6265 11/19/2012 11:48 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: place: Removed placecode to prevent datasources from creating duplicate entries for the same place, with different placecodes. This was a problem with the original BIEN2 geoscrub dataset, which contained duplicates.

6264 11/19/2012 10:54 AM Aaron Marcuse-Kubitza

inputs/import.stats.xls: Updated import times

6263 11/16/2012 07:06 PM Aaron Marcuse-Kubitza

Regenerated vegbien.ERD exports

6262 11/16/2012 07:03 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Fixed bug where need to join taxonoccurrence.collector_id to party because it's now an fkey rather than a literal name

6261 11/16/2012 06:58 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_*: Added coordinateUncertaintyInMeters

6260 11/16/2012 06:34 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Join to newWorldCountries on 2-digit ISO code instead of country name, to increase (BIEN2) newWorldCountries and GADM overlap