db_xml.py: put(): put_(): Support setDefault() values which are text nodes, by passing text strings through when put() is run on all col_defaults entries

db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names

dicts.py: DictProxy: Implemented delitem()

bin/map: update_in_label(): Removed hardcoded source_id col_default, which is now set in mappings/VegCore-VegBIEN.csv's output root

mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()

db_xml.py: put(): Added _setDefault() built-in function, which adds an entry to col_defaults

xml_func.py: _env(): Fixed bug where need to retrieve actual string value of name param using xml_dom.NodeTextEntryIter instead of NodeEntryIter

xml_func.py: _env(): Fixed bug where need to use xml_dom.replace_with_text() instead of xml_dom.replace() because replace() requires a DOM node

bin/map: update_in_label(): Set $source env var to the in_label (datasource name), to make it available to _env()

xml_func.py: Simplifying functions: Added _env()

Added inputs/VegBank/Source/, containing referenceType metadata

Added inputs/SpeciesLink/Source/, containing referenceType metadata

Added inputs/SALVIAS*/Source/, containing referenceType metadata

Added inputs/REMIB/Source/, containing referenceType metadata

Added inputs/GBIF/Source/, containing referenceType metadata

Added inputs/TEAM/Source/, containing referenceType metadata

Placed inputs/TEAM/_src/Vegetation-Tree-and-Liana-Metadata-1.5.pdf under version control

inputs/FIA/import_order.txt: Added Source, which needs to come before Organism

Added inputs/Madidi/Source/, containing referenceType metadata

Added inputs/FIA/Source/, containing referenceType metadata

Added inputs/CVS/Source/, containing referenceType metadata

Added inputs/CTFS/Source/, containing referenceType metadata

bin/map: Support map spreadsheets containing only metadata mappings (with no corresponding staging table), by falling back to an empty table when the named table does not exist

mappings/VegCore-VegBIEN.csv: institutionCode: Also map to the sourcename's matched source, which identifies whether the source is a herbarium

schemas/vegbien.sql: source: Made shortname NOT NULL to ensure that all datasources have a globally-unique short name

import_all: Added import of inputs/.herbaria/ before the main import

Added inputs/.herbaria/

input.Makefile: SVN: add: Also run %/add on all data subdirs

input.Makefile: Existing maps discovery: Moved tables discovery to its own section, above SVN so it can be used by SVN

mappings/VegCore.csv: referenceType: Fixed sort order

mappings/VegCore-VegBIEN.csv: Mapped referenceType

mappings/VegCore.csv: Added referenceType

mappings/VegCore-VegBIEN.csv: institutionCode: Remap to source.shortname when specimen information is not provided, as is the case for geoscrub.herbaria on nimoy

inputs/bien_web/observation/map.csv: Mapped observationID->occurrenceID

README.TXT: Datasource setup: Add input data for each table present in the datasource: Added step to run `make inputs/<datasrc>/<table>/install` if the table is in a .sql export

README.TXT: Datasource setup: MySQL inputs: Added step to install the export, which needs to happen before mapping individual tables

README.TXT: Datasource setup: Add input data for each table present in the datasource: Replaced "CSV" with "CSV" because there can be multiple CSV part files for one table

README.TXT: Datasource setup: Add input data for each table present in the datasource: Don't add a CSV or create.sql file for tables that are in a .sql export

README.TXT: Schema changes: Sync ERD with vegbien.sql schema: Changed instructions to just select tables with arrows next to them rather than all tables, because each table that's updated will have its lines reset and the number of lines that need to be fixed should be minimized

README.TXT: Datasource setup: Accept the test cases: `make inputs/<datasrc>/test by_col=1`: Clarified that errors could indicate bugs in the VegBIEN unique constraints

README.TXT: Data import: To remake analytical DB: Added explicit public schema setting since the analytical DB is often manually remade after the public schema has been renamed. Removed warnings that certain commands must be run after running make_analytical_db, because the "remake analytical DB" instructions no longer require this.

README.TXT: Datasource setup: MySQL inputs: Added steps to export the database to a PostgreSQL-compatible .sql file, which can be directly used by the install process without the need to export each table as CSV

README.TXT: Datasource setup: Choosing a table name: Documented that for .sql exports, you must use the name of the table in the DB export, not a suggested or custom name

input.Makefile: Staging tables installation: $(dbExports): Also include the files that would be generated by running _MySQL/*.make and creating the corresponding PostgreSQL translations

input.Makefile: Staging tables installation: Moved .sql export downloading and translation to separate Input data retrieval section

Added lib/MySQL.{data,schema}.sql.make templates to use in datasources' _MySQL/ dirs

inputs/import.stats.xls: Updated import times

schemas/vegbien.sql: analytical_stem_view: scientificNameWithMorphospecies: Changed to use Brad's formula, which concatenates genus and specific_epithet/morphospecies, and uses family if just the family is present, rather than using the full taxonomic name

mappings/VegCore-VegBIEN.csv: Concatenated taxonlabel: Don't prepend family if the taxonName/scientificName itself is the family, so that the family is not duplicated in the concatenated taxonomic name

schemas/functions.sql: _nullIf(): Removed NOT NULL constraint on null param, to support use a (nullable) column rather than a literal as the null-equivalent value

xml_func.py: Simplifying functions: Added _nullIf(), to remove calls with no null value

xml_dom.py: Added prune_parent()

schemas/functions.sql: Added _or()

schemas/functions.sql: Added _merge_words()

schemas/vegbien.sql: analytical_*: Renamed geosourceValid to geovalid. (It had gotten renamed in the reference -> source rename.)

mappings/VegCore.csv: Renamed georeferenceValid to geovalid

inputs/import.stats.xls: Updated import times. This now includes the Canadensys plants-related datasources HIBG, JBM, QFA, TRT, TRTE, UBC, VASCAN, and WIN.

inputs/import.stats.xls: Updated import times

Added inputs/HIBG/

Added inputs/JBM/

Added inputs/VASCAN/

Added inputs/WIN/

Added inputs/UBC/

Added inputs/TRTE/Specimen/

Added inputs/QFA/

Added inputs/TRT/

schemas/vegbien.sql: Allow bien_read to SELECT from all tables in the public schema

schemas/vegbien.sql: Allow bien_read to SELECT from analytical_aggregate, analytical_stem

lib/PostgreSQL-MySQL.csv: Removed GRANT/REVOKE because SCHEMA GRANTs are not supported in MySQL

pg_dump_vegbien: non-$owners mode: Removed --no-privileges in order to include GRANTs to other users

root Makefile: PostgreSQL: $(postgresReload-Linux): Making schemas/*.conf world-readable: Fixed bug where need to do this as the bien user, which owns the files

root Makefile: PostgreSQL: $(postgresReload-*): Make schemas/*.conf world-readable so it's readable by the postgres user, which the .conf installation is run as

root Makefile: PostgreSQL: $(postgresReload-*): Also install pg_hba.conf

root Makefile: PostgreSQL: Added postgres_reload to reload postgresql.conf and restart the DB

root Makefile: PostgreSQL: postgres-*: Factored postgresql.conf installation out in to $(postgresReload-*)

schemas/: Synced pg_hba.conf and pg_hba.Mac.conf's bien entries, which adds phpPgAdmin support (template1 access) on the Mac and bien_read access on Linux

root Makefile: VegBIEN DB: DB and users: Also create bien_read user for read-only access to the DB

schemas/pg_hba.Mac.conf: Allow access to the bien group rather than just the bien user, which will include bien_read

schemas/pg_hba.Mac.conf: Fixed bug where also need to allow password-based logins from the same machine, in order to work with pgAdmin

schemas/vegbien.ERD.poster.pdf: Updated to 33x51in poster size and 0.25in margins

README.TXT: Schema changes: Creating a poster of the ERD: Added section with the State St FedEx Kinkos' rates for posters ($10.25/sq ft laminated)

README.TXT: Schema changes: Creating a poster of the ERD: Changed "Measure the fractional height of the text onscreen" to "Determine the poster size"

Added schemas/vegbien.ERD.poster.pdf

Added schemas/vegbien.ERD.poster.core.print_options.png

Added schemas/vegbien.ERD.poster.core.pdf

schemas/pg_hba.Mac.conf: Fixed bug where needed ident entry for postgres superuser

Added config/bien_read_password

README.TXT: Schema changes: Added instructions to calculate the minimum VegBIEN poster size (to make the text as least as big as on the VegBank ERD poster), which is 35x54in portrait

schemas/vegbien.sql: analytical_stem_view: cultivated: Use location.iscultivated when taxonoccurrence.iscultivated is not available

Added inputs/FIA/FIA_COND_unique/, which contains the oldgrowth flag

mappings/VegCore-VegBIEN.csv: Mapped oldGrowth

schemas/functions.sql: Added _not()

mappings/VegCore.csv: Added oldGrowth

mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot

mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot

schemas/vegbien.sql: location: Added iscultivated for cases when entire plots rather than individual taxonoccurrences are marked as cultivated

inputs/FIA/: Added FIA_COND table from nimoy.geoscrub and code to generate a unique plot table from it, including the oldgrowth calculated field

Added inputs/FIA/Organism/postprocess.sql to cast PlotCD to a bigint

my2pg: Also remove (#) after bigint

Regenerated vegbien.ERD exports