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

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&gt;)

mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions

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

inputs/FIA/_src/: Added attachments from Brad's e-mail on 2013-2-8

xml_func.py: Removed no longer used _range(). Use SQL functions._range() instead.

schemas/functions.sql: Added _range()

xml_func.py: Removed no longer used _avg(). Use SQL functions._avg() instead.

schemas/functions.sql: Added _avg()

mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions

schemas/functions.sql: _dms_to_dd(text): Corrected concatenated form to interpret last 5 digits as MMmmm = MM.mmm instead of MMSSS, per Tom Wendt's explanation that this form is "degrees/minutes/decimalminutes"