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

schemas/vegbien.sql: Added _dms_to_dd()

inputs/bien2_traits/TraitObservation/map.csv: Remapped Source to sourceType

Added inputs/TEX/

units.py: convert(): Support ranges

Moved parse_range() from xml_func.py to units.py

units.py: conversions: Added ft->m conversion

src_map: Reopen stdin (/dev/stdin) in universal newlines mode to support files with \r as the line ending

csv2db: Open input stream in universal newlines mode to support files with \r as the line ending

mappings/VegCore.htm: Regenerated from wiki. Moved Forming IDs section to separate Global IDs wiki page (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs).

input.Makefile: $(exts): Added .tab

mappings/VegCore.htm: Regenerated from wiki. Moved preferred ID order to Forming IDs section as examples list. Made examples globally unique by prefixing the outer ID that scopes the value.

mappings/VegCore.htm: Regenerated from wiki. Forming IDs: Added instructions for making a local ID global. Added note that these globally unique IDs are not the same as UUIDs. Forming preferred IDs: Reworded as a set of instructions rather than a definition. Clarified that this becomes the database primary key.

mappings/VegCore.htm: Regenerated from wiki. Added section on forming preferred IDs, which are the ID which is most directly associated with the identified object.

mappings/VegCore.htm: Regenerated from wiki. Documentation has been added on how to choose term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming) and how to form globally unique ID values (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Forming-IDs). Source and Specimen terms have been renamed to be self-explanatory and unambiguous (the DwC equivalents remain as synonyms). Short definitions of Source terms have been added to explain the differences between them. Source, Specimen, and Collection terms have been shortened according to the new instructions for choosing preferred term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming).

inputs/NY/Ecatalog_all/test.xml.ref: Updated inserted row count

schemas/vegbien.sql: analytical_stem_view: scientificName_verbatim: Use the taxonname (which omits the family and author) instead when available, at Brad's request

schemas/vegbien.sql: Disambiguated taxonlabel.taxonomicname, taxonverbatim.taxonomicname, and taxonverbatim.taxonname

schemas/vegbien.sql: taxon_trait_view: Use taxonverbatim.taxonname (the binomial) in preference to taxonverbatim.taxonomicname (the binomial+author) or taxonlabel.taxonomicname (the family+binomial+author), at Mark's request

to_do/timeline.2013.xls: Obtain and load any additional new data: Extended beyond April because it's ongoing

README.TXT: Full database import: On nimoy: Moved analytical_aggregate table creation right after analytical_aggregate..csv download because it can happen while the file is downloaded

to_do/timeline.2013.xls: Reload existing data in need of refresh: Added additional cell because this is still in progress

to_do/timeline.2013.xls: Placed check mark in completed cells. Multi-cell tasks that are partially complete have check marks in part of their cells to indicate this.

Added inputs/FIA/REF_*/

inputs/FIA/_src/Makefile: Table bundling: Also unpack FIADB_REFERENCE/

Added inputs/FIA/_src/FIADB_REFERENCE.ZIP.md5, .url

schemas/vegbien.sql: provider_count_view: Group data by dataprovider and dataset, rather than by each separately, to satisfy the GBIF attribution requirements as described by Brad

schemas/vegbien.sql: analytical_plot/specimen: Moved threatened_bien after growthForm as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#SpeciesLink>

schemas/vegbien.sql: analytical_stem_view: Moved threatened_bien after growthForm as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#SpeciesLink>

schemas/vegbien.sql: sync_analytical_stem_to_view(): Also drop and re-create new dependent views analytical_plot, analytical_specimen

inputs/TEAM/V*/map.csv: Mapped plotArea_ha based on "1ha Plot Number" field name

inputs/TEAM/V*/map.csv: Id: Remapped to individualObservationID

mappings/VegCore.htm: Regenerated from wiki. verbatimScientificName, verbatimTaxonName have been merged into concatenatedScientificName, and ID has been disambiguated.

inputs/*/*/map.csv: Automapped taxonConfidence

schemas/vegbien.sql: analytical_stem_view: plotArea_ha: Fixed bug where need to use parent plot's area when subplot's area is not provided

inputs/SALVIAS/plotMetadata_/create.sql: Added primary key

inputs/NY/NY_DATA_20130212.~.utils.sql: pkey: Made table an enum instead of a text field so that Ecatalog_LatLong could be sorted before Ecatalog

inputs/NY/Ecatalog_all/create.sql: primary key: Combine table, key into one value so that the primary key has a single column. This is necessary because multi-column primary keys are not supported by the import algorithm.

inputs/NY/NY_DATA_20130212.~.utils.sql: Added pkey record type for use by Ecatalog_all's generated pkey

inputs/NY/Ecatalog_all/create.sql: Add table column which scopes the key field. Add primary key to allow sorting by it. inputs/NY/Ecatalog_all/map.csv: Documented that UniqueNYInternalRecordNumber is sometimes duplicated.

make_analytical_db: Wait for tnrs.make to acquire the tnrs.make lock if being run right after import

schemas/vegbien.sql: analytical_stem_view: taxonName_matched: Fixed bug where need to use the matched_taxonverbatim instead of the datasource_taxonverbatim

Moved wait on tnrs.make lock from import_all to make_analytical_db, so that running make_analytical_db for a one-time import also waits on the lock

schemas/vegbien.sql: taxondetermination: taxondetermination_unique: Added determinationtype so that when the matched and accepted determinations are the same, they still both get created rather than the second one being removed due to the unique constraint

schemas/vegbien.sql: analytical_specimen: Removed speciesBinomialWithMorphospecies because it doesn't apply to specimens

schemas/vegbien.sql: Added analytical_plot view

schemas/vegbien.sql: Added analytical_specimen view

schemas/vegbien.sql: analytical_stem_view: Moved recordedBy, recordNumber before dateCollected as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#ACAD>

schemas/vegbien.ERD.mwb: Synced with schema

schemas/vegbien.sql: Added reproductiveCondition

mappings/VegCore-VegBIEN.csv: Mapped reproductiveCondition

schemas/vegbien.sql: plantobservation: Added reproductivecondition

mappings/VegCore.htm: Regenerated from wiki. matched*Fit_fraction has been renamed to matched*Confidence_fraction.

inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Updated for new mappings/VegCore.htm

inputs/bien_web/observation/map.csv: Re-automapped taxonMorphospecies

mappings/VegCore.htm: Regenerated from wiki. Data owner terms and taxon synonyms have been added, and morphospecies has been disambiguated.

schemas/vegbien.sql: analytical_stem_view: Moved identifiedBy, dateIdentified, identificationRemarks right after the *_verbatim terms that they relate to, as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#ACAD>

schemas/vegbien.sql: analytical_stem_view: Use new concat_delim() instead of array_to_string() surrounded by NULLIF

schemas/vegbien.sql: Added concat_delim()

schemas/vegbien.sql: analytical_stem_view: Removed deprecated taxonNameWithMorphospecies now that we have speciesBinomialWithMorphospecies

schemas/vegbien.sql: analytical_stem_view: speciesBinomial: Added morphospecies suffix to create speciesBinomialWithMorphospecies

inputs/import.stats.xls: Updated import times

README.TXT: Full database import: Check that unscrubbed_taxondetermination_view returns no rows: Documented that this takes 90 s with LIMIT 1

schemas/vegbien.sql: _taxon_family_require_std(): Also allow non-aceae families accepted by TNRS

Added inputs/SALVIAS/_archive/salvias_plots.*.sql.zip.md5

Added inputs/VegBank/_archive/vegbank_for_bien.tar.gz.url

Added inputs/U/UtrechtHerbarium.csv.tar.gz.url

Added inputs/TEAM/_archive/ci-team_extract.tar.gz.url

Added inputs/SpeciesLink/_archive/specieslink*.txt.gz.url

Added inputs/REMIB/_archive/remib_raw.csv.tar.gz.url

Added inputs/NY/NYSpecimenDataAmericas.csv.tar.gz.url

Added inputs/NCU/_archive/NCU-NCSC_2010-02-12.csv.tar.gz.url

Added inputs/MO/mo_digirexport.tar.gz.url

Added inputs/Madidi/_archive/2010-1-2/madidi_plots_original_12jan2010.zip.url

Added inputs/GBIF/gbif_extract.tar.gz.url

Added inputs/FIA/fia_extract.tar.gz.url

Added inputs/CVS/_archive/CVS-allTaxonOccurrences_2010-01-12.txt.tar.gz.url

Added inputs/ARIZ/ARIZ_DiGIR_21012010.csv.tar.gz.url

Added inputs/UNCC/Specimen/UNCC.csv.url, UNCC.csv.md5

Added inputs/XAL/_src/digir.xml.gz.md5

Added inputs/UNCC/_src/ with UNCC.csv.zip.md5

Added inputs/SpeciesLink/_src

README.TXT: Datasource setup: MySQL inputs: .sql exports: Use new mysql_bien to connect to the MySQL DB created for the datasource

Added mysql_bien, which runs a MySQL command on the local MySQL server

Added inputs/GBIF/_src/GBIFPortalDB-2012-12-11.dump.md5 (md5sum of the expanded file)

root Makefile: MySQL: mysql-Linux: Also install phpMyAdmin

root Makefile: MySQL: mysql-Linux: Split apt-get dependencies into separate commands, like for other apt-get commands, to avoid having one failed dependency prevent the following dependencies from being installed

root Makefile: MySQL: *mysql_users: Also add bien_read user

root Makefile: MySQL: Renamed *mysql_user to *mysql_users because there can be multiple users

inputs/: Added .md5 files for all .zip, .gz

Added inputs/HVAA/Specimen/Herbario_occur_1360871068.csv.url

lib/common.Makefile: rsync: $(rsync*): Use --no-group because the file group is different depending on the machine