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>)
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()
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"
inputs/MO/Specimen/postprocess.sql: Use :table instead of hardcoding "MO"."Specimen"
inputs/MO/Specimen/postprocess.sql: Also remove frameshifted rows where InstitutionCode is NULL
inputs/UNCC/Specimen/map.csv: herbarium->specimenIndexer: Replace UNCCD (UNCC database?) with UNCC
schemas/functions.sql: functions._dms_to_dd(): Added support for DMS values without separators
README.TXT: Datasource setup: Update vegbiendev: Removed command to run the tests on vegbiendev because vegbiendev no longer has an empty public schema for running tests on (the public schema instead contains the latest published import)
Mapped inputs/BRIT/
my2pg: Remove (0) after char
my2pg: Remove any (#) after bytea
my2pg: Translate binary to bytea
README.TXT: Datasource setup: MySQL inputs: Editing _MySQL/*.make: Set $server to vegbiendev instead so the export command will work from any machine (though it will be faster from vegbiendev itself)
inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where needs to be set to just localhost and --user to bien instead
README.TXT: Datasource setup: MySQL inputs: Editing _MySQL/*.make: Fixed bug where $server needs to be set to just localhost and --user to bien instead.
lib/MySQL.*.sql.make: Added --user option to demonstrate how to set the DB user vs. the ssh user