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

input.Makefile: SVN: $(_svnFilesGlob): Also add .md5 files. This allows svn to track where unversioned files should be in the directory tree.

input.Makefile: SVN: $(_svnFilesGlob): .url, .pdf, and README.TXT in the top-level dir: Fixed bug where had extra / after brace expr

input.Makefile: SVN: $(_svnFilesGlob): Also add .url, .pdf, and README.TXT in the top-level dir

input.Makefile: SVN: $(_svnFilesGlob): Add .url, .pdf, and README.TXT files in all subdirs, not just _src

lib/common.Makefile: remote server: Use jupiter instead of vegbiendev, to ensure that all files get uploaded there rather than only to vegbiendev. This involves adding an extra database import step to download the uploaded files from jupiter onto vegbiendev.

inputs/FIA/_src/Makefile: all: Extract zip files before running tables target, because it requires the created dirs

schemas/vegbien.ERD.mwb: Fixed table sizes

Removed no longer used fix_permissions. Use root fix_perms instead.

Added root fix_perms

Moved Checksums from backups/Makefile to lib/common.Makefile so all dirs (including inputs/) can use md5sum testing

lib/common.Makefile: $(remote): Made remote basepath configurable in $(remote_basepath)

lib/common.Makefile: Renamed $(src_server) to $(remote_host) and $(src_user) to $(remote_user) for clarity

inputs/GBIF/: Added refresh metadata

Added inputs/HVAA/

Added inputs/ARIZ/_archive

inputs/ARIZ/: Removed previous data now that it has been refreshed

inputs/ARIZ/: Mapped refresh

Added inputs/ARIZ/import_order.txt

Added inputs/NY/_archive/

inputs/NY/: Removed tables from previous extract

inputs/NY/: Mapped refresh

inputs/*/*/VegBIEN.csv: Regenerated from mappings/VegCore-VegBIEN.csv

Added inputs/NY/import_order.txt

inputs/ARIZ/: Added SQL export for refresh

my2pg.data: Translate indefinite (zero) months which have a definite day. This is unusual, but does appear in some data such as the ARIZ DB.

my2pg.data: Translate indefinite dates (dates with 0 as the month or day)

my2pg: Use my2pg.data to perform data-only replacements, instead of duplicating them in both my2pg and my2pg.data

my2pg: named UNIQUE KEYs: Comment out the name because PostgreSQL requires it to be globally unique, but MySQL only requires it to be unique within the table

my2pg: Translate UNIQUE KEYs instead of removing them

my2pg*: Removed KEYs: Comment out the definition rather than removing it

my2pg*: Remove FOREIGN KEYs because MySQL does not dump tables in dependency order, which prevents PostgreSQL from creating tables whose fkeys refer to a later table

my2pg*: Replacing invalid table elements to remove them: Use a dummy CHECK constraint instead of a boolean field to avoid adding fields to the table. The elements can't always simply be removed because sed can't remove the trailing comma of the previous element, and removing the following comma doesn't work for the last element in the table.

my2pg*: Replace '0000-00-00 00:00:00' with '-infinity'

my2pg: Replace datetime with timestamp

my2pg: Remove COLLATE field attribute

lib/MySQL.*.sql.make: Documented that $server user/host are for ssh, not the DB

lib/MySQL.*.sql.make: Documented that $server can also contain a username (which will be used by ssh)

my2pg_export: Use the --quick option to facilitate exporting large tables (it avoids retrieving all rows before outputting any of them)

README.TXT: Datasource setup: Added instructions for MS Access databases