Removed inputs/GBIF/_src/GBIFPortalDB-2012-12-11.dump*, which has been replaced by GBIFPortalDB-2013-02-20.dump

mappings/VegCore.htm: Regenerated from wiki. Renamed MatchedTaxonDetermination/AcceptedTaxonDetermination to MatchedTaxon/AcceptedTaxon because they relate to a taxon name rather than to an application of that name to a TaxonOccurrence

schemas/functions.sql: functions._map(): Made function STRICT because it always returns NULL if either argument is NULL

inputs/UNCC/Specimen/map.csv: campus: Mapped to cultivated, interpreting non-NULL values as true

inputs/UNCC/Specimen/map.csv: campus: Removed mapping to occurrenceRemarks because this is just a code, not a description. Added definition from Bob's validation comments.

inputs/UNCC/Specimen/map.csv: accession: Removed comment that this is actually the catalogNumber, because they are now synonyms

mappings/VegCore.htm: Regenerated from wiki. Split specimenIndexer into specimenStampingInstitution and specimenDonor (which are often the same).

mappings/VegCore-VegBIEN.csv: Removed specimenIndexer->institutionCode mappings because the institutionCode should refer only to the specimenHolder

Added inputs/GBIF/_src/GBIFPortalDB-2013-02-20.dump.gz (a new download they posted to the FTP site)

schemas/vegbien.sql: analytical_specimen: Removed growthForm, threatened_bien at Brad's request (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#UNCC > Brad Boyle's comments > growthForm, threatened_bien)

inputs/UNCC/Specimen/map.csv: Removed mappings to reproductiveCondition because we don't know what the single-letter codes mean

inputs/UNCC/Specimen/map.csv: Fixed embedded line endings

schemas/vegbien.sql: _locationnarrative_is_cultivated(): Fixed bug where need to use NULL instead of false (and bool_or() instead of OR) for a non-match, because the absence of a match doesn't mean it's not cultivated

mappings/VegCore.htm: Regenerated from wiki. Editing: Changed ambiguous terms templates to list the name of the alternative itself in the alternatives list, instead of the ambiguous term + a source suffix. This avoids the need to choose a source suffix for each alternative of an ambiguous term, as the ambiguous term itself (without the suffix) can be listed as the synonym. Coordinates: Disambiguated verbatimCoordinateSystem.

mappings/Makefile: VegCore.thesaurus.csv: `uniq`ify the map after applying initial translations, to support mappings that appear twice (once as the result of an alternative's synonym entry and again as the result of an ambiguous term's alternatives listing)

schemas/vegbien.sql: analytical_stem_view: Added temperature_C, precipitation_m for possible use in John Wiens' plant climatic niche evolution project ("how fast is the rate of climatic niche evolution among species compared to projected changes in climate over the next 100 years? How do these rates compare for temperature and precipitation variables?")

mappings/VegCore.htm: Regenerated from wiki. Added specimenDescription.

mappings/VegCore.htm: Regenerated from wiki. Split apart identificationQualifier and taxonFit. Split apart taxonConfidence and identificationVerificationStatus. Moved identificationQualifier to new QualifiedTaxonName table.

README.TXT: Full database import: To view progress: Use tail -100 to show more of the log files, and not tail -f to avoid blocking when the user just wants to check the status

inputs/BRIT/specimen_flat/map.csv: Only map Notes_Plant to occurrenceRemarks if there is a separate Locality_Description, in order to filter out Notes_Plant values that concatenate everything together (often including a herbarium name that would mess up the cultivated flag parsing)

my2pg.data: Replace \0 (with the backslash) with 0 because \0 isn't allowed in UTF-8

root Makefile: VegBIEN DB: mk_db: Added command to import arbitrary DB users from a config file

inputs/import.stats.xls: Updated import times

inputs/TEX/Specimen2/map.csv: _join() PLANT DATA and MISC NOTES to form occurrenceRemarks instead of _alt()ing them

inputs/TEX/Specimen2/test.xml.ref: Accepted test

inputs/BRIT/_MySQL/MySQL.*.sql.make: Include all tables, not just specimen_flat

my2pg: Replace tinytext, mediumtext with text

Added inputs/GBIF/_src/_README.TXT with Brad's GBIF filtering rules

inputs/FIA/TREE/postprocess.sql: Use :table instead of hardcoding the table name

inputs/FIA/*/postprocess.sql: UNIQUE constraint: Added UNITCD because although it may not be needed to scope PLOT, it is present in all the core tables and thus must be part of the joins' USING columns

inputs/FIA/*/postprocess.sql for core tables: Added unique constraint on the datasource's primary key fields

Added inputs/CTFS/AggregateObservation/ from BIEN2 data

inputs/CTFS/: Switched global _no_import to table-specific _no_imports to allow adding new tables that are imported

Added schemas/TAPIR/SpeciesLink.tapir_request.txt symlink

Added inputs/SpeciesLink/_src/tapir_request.txt

Added schemas/TAPIR/

Added planning/use_cases/rare_species.png

Added planning/goals/BIEN deliverables.png

Added planning/resources/iPlant_Overview_BIEN_2011.pdf.url

planning/goals/Enquist_BIEN_Overview_2011.pptx: Replaced with .url file. Note that the Plone site <http://groups.nceas.ucsb.edu/bien/meetings> is not searchable by document filename.

Added planning/workflow/Boyle_BIEN_data_quality.pdf.url

Added planning/goals/BIEN_Science_2011.pptx.url, BIEN-Tech-Oct2011.ppt.url, Enquist_BIEN_Overview_2011.pptx

Added schemas/VegX/run.py

Added schemas/VegBIEN/growth_forms/Barbara_Dobrin.parsing.scripts/

Added schemas/VegX/Veg-X_paper_in_press_Applied_Vegetation_Science.pdf.url

Added schemas/VegX/JVS-VegX.pdf.url

Added schemas/VegBank/VegBank_Data_Model.with_Collections_intro.ppt

Added planning/goals/BIEN_White_Paper.pdf.url

Added planning/meetings/2010-12-08.working_group/BIEN3-plan.docx

Added schemas/VegBIEN/planning/taxonomy/On_the_Use_of_Taxonomic_Concepts_in_Support_of_Biodiversity_Research_and_Taxonomy.pdf.url

Added schemas/BIEN2/ERD/

Added schemas/BIEN2/bien2_core_schema.png

Added schemas/BIEN2/mappings/BIEN2.viewFullOccurrence-DwC.xls

Added schemas/VegBank/mappings/VegBank.observation-VegX.plotObservation.xls

schemas/vegbien.ERD.mwb: Fixed table positions due to plantobservation field addition

Added schemas/DiGIR/gbif-occurrencestore.digir.client.url

Added schemas/DiGIR/gbif-crawler.digir.*.url

inputs/.geoscrub/import_order.txt: Added Source

Added schemas/VegX/

Added schemas/VegBIEN/taxonomy/family_higher_plant_group.sql

Added planning/use_cases/Trait_BIEN_data_use_case.docx

Added planning/workflow/2010.working_group.white_board/

Added planning/milestones/_archive/BIEN3 Milestones and Development Timeline_MLN2.*

Added planning/workflow/BIEN-modArch-Dec2010 NS-SBD 1.4.ppt

Added planning/milestones/_archive/BIEN3_milestones.2011-12-13.doc

Added planning/milestones/BIEN Milestone – feedback.docx

Added schemas/VegBIEN/planning/taxonomy/Nomenclature_excerpt.ppt

Added planning/use_cases/

Added planning/meetings/2012-11-26~30.working_group/

Added schemas/BIEN2/Guide_to_the_BIEN2_database.pdf

Added planning/meetings/2011-10-24~28.working_group/

Added schemas/VegBIEN/planning/BIEN_OctWG-Whtbrd*.jpg

Added schemas/BIEN2/

Added schemas/VegBIEN/

Moved schemas/vegbank.* to schemas/VegBank/

Added planning/milestones/BIEN3 - Progress since the 2011 working group.docx

planning/meetings/: Added Martha's conference call notes

Moved planning/milestones.doc to planning/milestones/

Moved planning/timeline.* to timeline/

Renamed to_do/ to planning/

Added schemas/VegCore/

Added schemas/DwC/

Added schemas/BIEN_logo.png from the bien.nceas.ucsb.edu website

Renamed schemas/BIEN_logo.png to BIEN_logo.small.png

Added inputs/SALVIAS/_archive/salvias_bien_19nov2009.tar.gz.url, .md5

Added inputs/REMIB/_archive/remib_raw.0.header.specimens.txt

Added inputs/CTFS/_src/ctfs_extract.tab.url, .md5

Added inputs/NVS/_src/NVS_VegX.XSLT, _src/VegX/

Added inputs/NVS/_src/_README.TXT

Added inputs/TurboVeg/_src/DBASEDIC_rkp2011*.xlsx

Added inputs/TurboVeg/_src/_README.TXT

inputs/import.stats.xls: Updated import times

README.TXT: Full database import: Don't run backups/fix_perms with sudo because owners are not rsynced to jupiter, so fixing them first is unnecessary. (It's not necessary to change the file owner to bien at any other time, either, because commands are not run as the bien user. It's in fact better to leave the file owner as yourself, to allow rsync to set the modification times.)

README.TXT: Full database import: Added steps to set $version in all vegbiendev terminals

lib/common.Makefile: rsync: $(rsync): Also exclude .lk* lock files

README.TXT: Full database import: Updated log file sync steps for syncing via jupiter

inputs/BRIT/specimen_flat/test.xml.ref: Updated inserted row count

schemas/py_functions.sql: Added _date(year integer, month integer, day integer)

inputs/BRIT/specimen_flat/postprocess.sql: Added primary key

schemas/functions.sql: Added _dms_to_dd() that takes text arguments and casts them to the appropriate type