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
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
inputs/HVAA/Specimen/map.csv: Remapped fieldNotes to UNUSED. This also fixes a bug where fieldNotes was colliding with other occurrenceRemarks inputs because it was missing a filter.
schemas/vegbien.sql: analytical_specimen/analytical_plot: Added occurrenceRemarks
inputs/REMIB/Specimen/map.csv: Mapping NULL-equivalent lat/long to NULL: Fixed bug where need special *=* mapping to pass through values not in the map
inputs/REMIB/Specimen/map.csv: Map NULL-equivalent text fields (country, state, etc.) to NULL
inputs/REMIB/Specimen/map.csv: Map NULL-equivalent lat/long to NULL
inputs/SpeciesLink/Specimen/map.csv: dwc_dwcore_Remarks: Remapped to occurrenceRemarks (it had been incorrectly automapped to taxonRemarks). Combined occurrenceRemarks inputs using /_alt.
mappings/VegCore.htm: Regenerated from wiki. Remapped organismNotes to be a synonym of occurrenceRemarks, since notes on an organism are more generally notes on an occurrence.
inputs/HVAA/Specimen/map.csv: Remapped dynamicProperties to occurrenceRemarks because it contains occurrenceRemarks data
schemas/vegbien.sql: analytical_stem_view: Added occurrenceRemarks
mappings/VegCore-VegBIEN.csv: Mapped occurrenceRemarks
mappings/VegCore-VegBIEN.csv: Only use one of collection and collectionURL instead of concatenating them when both are provided (as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#ACAD>)
mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions
inputs/FIA/_src/_README.TXT: Added e-mail from Brad Boyle on 2013-2-8
