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"

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

inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where $server needs to be set to bien@localhost

README.TXT: Datasource setup: MySQL inputs: Editing _MySQL/*.make: Specified that $server needs to be set to bien@localhost. Install the staging tables: Specified that for a MySQL .sql export, this must be done on vegbiendev.

inputs/BRIT/: Added _MySQL/MySQL.*.sql.make

README.TXT: Datasource setup: MySQL inputs: .sql exports: Run mysql_bien in the background

README.TXT: Datasource setup: MySQL inputs: .sql exports: Added steps to sync the export to vegbiendev. Specified that the database for the MySQL export should be created on vegbiendev.

README.TXT: Datasource setup: Update vegbiendev: Updated steps for syncing via jupiter

Added inputs/BRIT/ (not yet translated to PostgreSQL)

mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_DMS to coordinates.latitude_deg using new _dms_to_dd(text)

mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_DMS to coordinates.latitude_deg using new _dms_to_dd(text)

schemas/functions.sql: Added _dms_to_dd(text)

schemas/functions.sql: _dms_to_dd(): Fixed bug where need to use 1 as the multiplier when dir is NULL

schemas/functions.sql: _dms_to_dd(): Fixed bug where need to apply the sign multiplier after the components are added, because it applies to the DMS as a whole rather than just to the degree component

README.TXT: Full database import: Before running `make inputs/upload`, added step to do ./fix_perms on local machine so that files are not uploaded to jupiter with incorrect permissions

README.TXT: Full database import: Before running `make inputs/upload`, added step to do svn up on jupiter so that unversioned files are not uploaded before their versioned equivalents are checked out from svn (requiring each file to be manually svn-added before the svn up can proceed)

schemas/functions.sql: _dms_to_dd(): Added dir param to specify compass dir suffix, in order to calculate the sign correctly

Moved compass_dir from schemas/vegbien.sql to schemas/functions.sql so it can be used by _dms_to_dd()

Moved _dms_to_dd() from schemas/vegbien.sql to schemas/functions.sql so it can use functions schema functions

schemas/vegbien.sql: Added compass_dir enum

inputs/TEX/Specimen/map.csv: Remapped LAT/LONG_DEGREES,MINUTES,SECONDS to new latitude/longitude_deg,min,sec, allowing the DMS coordinates to be translated

inputs/REMIB/Specimen/map.csv: Remapped lat/long_deg,min,sec to new latitude/longitude_deg,min,sec, allowing the DMS coordinates to be translated

mappings/VegCore-VegBIEN.csv: latitude/longitude_deg,min,sec: Also mapped to the geoscrub coordinates entry

mappings/VegCore-VegBIEN.csv: latitude/longitude_sec: Fixed name, which had been incorrectly automapped to verbatim*

mappings/VegCore.htm: Regenerated from wiki. latitude/longitude: Moved _deg,min,sec components after unit alternatives so that unit alternatives following them wouldn't incorrectly be interpreted as alternatives for the *components instead of for the overall, unitless term.

mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_deg,min,sec

mappings/VegCore.htm: Regenerated from wiki. Merged coordinateUncertainty and coordinatePrecision, since datasources often use these interchangeably (the only difference is the DwC-recommended units).

mappings/VegCore.htm: Regenerated from wiki. Source: Added authors. Renamed creator to firstPublisher. Moved dataOwner to Source as list. Coordinates: latitude/longitude, coordinatePrecision: Added units disambiguation. latitude/longitude_DMS: Added components. Global IDs: Changed "globally unique" tag to "global ID" and hyperlinked it to <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs> (which now includes detailed examples of the various types of global IDs).

inputs/SpeciesLink/Specimen/map.csv: conceptual_darwin_2003_1_0_CoordinatePrecision: Remapped to coordinateUncertaintyInMeters, assuming units based on the range and precision of values

inputs/HVAA/Specimen/map.csv: Remapped coordinatePrecision to UNUSED

inputs/ARIZ/omoccurrences/map.csv: Remapped coordinatePrecision to UNUSED