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

README.TXT: Datasource setup: MySQL inputs: Added instruction to skip the Add input data for each table section

inputs/NY/: Added SQL export for refresh

mappings/VegCore.htm: Regenerated from wiki. Brad's new DwC ID terms spreadsheet has now been added, and a number of the ID terms clarified, disambiguated, and recategorized. In particular, institutionCode has now been split into the custodialInstitutions and collectingInstitution, to differentiate between which institution has the specimen vs. stamped the specimen. This distinction is important because the catalogNumber, stamped on the specimen, is only unique within the collectingInstitution. Most datasources don't unambiguously specify which institution their institutionCode is referring to, so it has been assumed to be custodialInstitutions unless a data dictionary says otherwise (as is the case for UNCC). In addition, a MatchedTaxonDetermination table has been added with the *_matched fields from TNRS.

inputs/CVS/observation_/map.csv: baseSaturation: Resolved ambiguous term

mappings/Makefile: VegCore.vocab.csv: Ignore leading ? when sorting so that ambiguous terms sort alphabetically with other terms. This prevents terms from moving from their previous location when they become ambiguous.

Added sort_ci to sort a spreadsheet, ignoring leading punctuation

mappings/VegCore.vocab.csv: Changed line endings to \r\n in preparation for having a Python script run on it (which changes the line endings)

mappings/Makefile: VegCore.vocab.csv: Added back ambiguous terms, so that the vocabulary contains all terms defined by VegCore, regardless of whether they are ambiguous or unambiguous terms

mappings/Makefile: VegCore.vocab.csv: Added back synonyms, so that the vocabulary contains all terms defined by VegCore, regardless of whether they are synonyms or primary terms. This also prevents VegCore.vocab.csv from losing entries when terms are renamed, which made it difficult to verify that no terms were lost when refactoring.

inputs/MO/Specimen/postprocess.sql: Remove frameshifted rows by detecting InstitutionCodes without any letters

inputs/ARIZ/Specimen/map.csv: CollectorNumber/FieldNumber: Use /_first to map these identical fields to the same location

inputs/ARIZ/Specimen/map.csv: Fixed bug where the column names for InstitutionCode and CollectionCode were reversed in the source data

inputs/*/Specimen/map.csv for Canadensys sources: Remapped institutionID to UNUSED

mappings/VegCore.htm: Regenerated from wiki. The original*, accepted*, and verbatim* Taxon fields have now been moved to separate OriginalTaxonDetermination, AcceptedTaxonDetermination, and TaxonVerbatim tables.

mappings/VegCore.htm: Regenerated from wiki

mappings/VegCore.htm: Regenerated from wiki

README.TXT: Maintenance: VegCore data dictionary: Replaced VegCore.*.csv with VegCore.htm because now that VegCore.*.csv are sorted alphabetically, they generally don't change when VegCore.htm changes

mappings/VegCore.*.csv: Regenerated from wiki. A plain text label is now used for Replace with, which fixes a bug where the PRIVATE permalink pointed to its Replace with in realLatitude instead of its definition.

redmine_synonyms: Support plain text labels other than Alternative, such as Replace with

mappings/VegCore.*.csv: Regenerated from wiki. Alternatives now contain the "Alternative" label as plain text rather than as an image title, thus avoiding an HTML anchor conflict with the definition and allowing ambiguous terms to be placed before their alternatives as well as after.

README.TXT: Maintenance: VegCore data dictionary: Updated VegCore.csv filename to VegCore.*.csv

redmine_synonyms: Support alternatives which contain the "Alternative" label as plain text rather than as an image title. This is done to include the "Alternative" label in the HTML anchor and thus prevent the anchor from conflicting with the actual definition of the alternative (which would otherwise have the same anchor text). This allows ambiguous terms to be placed before their alternatives as well as after, because there won't be anchor conflicts that need to be resolved with careful ordering.

mappings/VegCore.csv: Regenerated from wiki. Taxon terms with prefixes for other TaxonDeterminations now indicate the analogous term in an "analogous to" label next to the term

mappings/VegCore.csv: Regenerated from wiki. Taxon terms with prefixes for other TaxonDeterminations now indicate the analogous term in an "analogous to" label next to the term

mappings/VegCore.csv: Regenerated from wiki. Taxon terms with prefixes for other TaxonDeterminations now indicate the analogous term in an "analogous to" label next to the term

mappings/VegCore-VegBIEN.csv: datasourceRecordID: Fixed bug where also need to add datasourceRecordID next to occurrenceID for an institutionCode remap switch

inputs/bien_web/observation/test.xml.ref: Regenerated

inputs/import.stats.xls: Updated import times using the import_times bugfix for times longer than a day