schemas/vegbien.sql: sourcecontributor: role: Changed type to role

schemas/vegbien.sql: role enum: Added VegBank data dictionary values from <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1331&entity=dba_fielddescription&params=1331>

schemas/vegbien.sql: sourcecontributor: Renamed position to order for consistency with the ERD definition <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=referencecontributor&entity=dba_tabledescription&where=where_tablename#position> and disambiguation from other meanings of position which are similar to role

schemas/vegbien.sql: sourcecontributor: Renamed roletype to role for consistency with the ERD definition <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=referencecontributor&entity=dba_tabledescription&where=where_tablename#roleType>

inputs/.geoscrub/geoscrub_output/map.csv: Mapped to county, acceptedCounty

mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place

mappings/VegCore.csv: Added acceptedCounty

schemas/pg_hba.Mac.conf: Changed to match schemas/pg_hba.conf

schemas/pg_hba.conf: Fixed bug where also need an IPv6 bien entry with md5 authentication, because the IPv4 md5 authentication does not apply to "localhost", which is translated to the IPv6 address ::1

schemas/pg_hba.conf: Fixed bug where also need a local bien entry with md5 authentication, because the host-based md5 authentication applies only to literal IP addresses, not "localhost"

Added schemas/pg_hba.Mac.conf

schemas/pg_hba.conf: Restrict all accesses to the server except the bien user accessing vegbien using ident or a password, and the postgres superuser logging in using ident

inputs/.geoscrub/geoscrub_output/map.csv: Mapped countyvalidity to latLongInCounty

schemas/functions.sql: _map(): Fixed bug where entries that map to NULL were incorrectly being treated as if the entry didn't exist. Note that -> returns NULL both if the entry's value is NULL and if the entry doesn't exist, so ? must be used to recheck the presence of the key in the hstore.

mappings/VegCore-VegBIEN.csv: Mapped latLongInCounty

mappings/VegCore.csv: Added latLongInCounty

schemas/vegbien.sql: Added distance_to_county_m. Note that this can also be used to store latLongInCounty by mapping true to 0 and false to -1.

schemas/pg_hba.conf: Changed trust authentication back to ident/md5. Not sure how it got set to trust since I used md5 when enabling remote access to the DB for the bien user.

Added schemas/pg_hba.conf

schemas/vegbien.sql: place: Removed placecode to prevent datasources from creating duplicate entries for the same place, with different placecodes. This was a problem with the original BIEN2 geoscrub dataset, which contained duplicates.

inputs/import.stats.xls: Updated import times

Regenerated vegbien.ERD exports

schemas/vegbien.sql: analytical_stem_view: Fixed bug where need to join taxonoccurrence.collector_id to party because it's now an fkey rather than a literal name

schemas/vegbien.sql: analytical_*: Added coordinateUncertaintyInMeters

schemas/vegbien.sql: analytical_stem_view: Join to newWorldCountries on 2-digit ISO code instead of country name, to increase (BIEN2) newWorldCountries and GADM overlap

psql_vegbien: Run with sh because it no longer needs bash support

psql_script_vegbien: Fixed bug where needs to be run with bash instead of sh

Added inputs/newWorld/iso_code_gadm/

Added inputs/newWorld/_src/

inputs/XAL/Specimen/map.csv: darwin:FieldNumber: Removed command to determine that field is unused, because UNUSED is a factual assertion that does not need a reason to be specified each time

inputs/XAL/Specimen/map.csv: Remapped darwin:CoordinatePrecision to UNUSED

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

mappings/VegCore.csv: coordinatePrecision: Added units (degrees) to form coordinatePrecision_deg

mappings/VegCore-VegBIEN.csv: Removed mapping for coordinatePrecision, which is not the same as coordsaccuracy_m. coordinatePrecision is instead "the precision of the coordinates" themselves in degrees (<http://rs.tdwg.org/dwc/terms/#coordinatePrecision&gt;).

schemas/vegbien.sql: coordinates: Changed coordinates.coordsaccuracy_deg units to m

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

schemas/vegbien.ERD.mwb: Added projectcontributor, locationeventcontributor to ERD

schemas/vegbien.sql: higher_plant_group_nodes: Added root->NULL mapping to store all the families that don't match any higher plant group

schemas/vegbien.sql: higher_plant_group_nodes: Allow NULL values for higher_plant_group, to allow mapping all remaining families to NULL in family_higher_plant_group

psql_vegbien: Fixed bug where did not display command prompt when run from command line, by moving automatic setting of search_path to psql_script_vegbien. psql_script_vegbien is now used instead of psql_vegbien wherever the search_path needs to be set, so removing this functionality from psql_vegbien is not a problem.

input.Makefile: BIEN commands: $(psqlAsBien): Use psql_script_vegbien, which automatically adds the $(psqlOpts), instead of psql_vegbien

schemas/functions.sql: _map(): Support any entry having the value '*' (not just the '*' entry), which passes through that value. Support an entry having the value '!', which raises an exception.

inputs/SALVIAS/plotMetadata_/map.csv: AccessCode: Removed _map entry for 4, which does not apply to plots

schemas/vegbien.ERD.mwb: Fixed lines

schemas/vegbien.sql: locationevent: Added accesslevel

inputs/SALVIAS/plotMetadata_/map.csv: Mapped AccessCode to dcterms:accessRights with appropriate _map filter

Added inputs/.geoscrub/geoscrub_cleaned_unique/_no_import to disable geoscrub_cleaned_unique, since the new geoscrub_output supersedes it

Added inputs/.geoscrub/geoscrub_output/

Added inputs/.geoscrub/_src/README.TXT

Regenerated inputs/bien_web/observation/VegBIEN.csv

Added inputs/.geoscrub/_src/ to store Jim's geoscrub CSV

schemas/functions.sql: _map(): Changed error message for an unmapped value to "Value not in map" rather than "Invalid map value", because an unmapped value is not necessarily explicitly invalid

inputs/VegBank/plot_/map.csv: confidentialitystatus filter: Merged mappings for 0 with other public-equivalent fields. Note that fuzzed plots are still public, because the private columns have been removed.

inputs/VegBank/plot_/map.csv: Mapped confidentialitystatus to dcterms:accessRights with an appropriate _map filter

mappings/VegCore-VegBIEN.csv: Mapped dcterms:accessRights

schemas/functions.sql: _map(): Raise data_exception if value not in map and no default provided (not the same as a NULL default value)

mappings/VegCore-VegBIEN.csv: verbatimGrowthForm: Removed _map filter, which applied only to SALVIAS and has now been moved to the applicable SALVIAS tables

inputs/SALVIAS*/plotObservations/map.csv: Remapped Habit to growthForm with _map filter applied

sql_io.py: put_table(): Special handling for functions with hstore params: Fixed bug where need to unwrap literal values of mapping, which might be sql_gen.Literal objects

sql_gen.py: Added get_value()

dicts.py: join(): Added support for unhashable types, which are passed through. This adds support for SQL literal values which are dicts (hstores).

xml_func.py: Removed no longer used _map(), which has been replaced by a corresponding DB function

schemas/functions.sql: Added _map(), which uses the new hstore functionality. This expands _map() functionality to column-based import.

root Makefile: VegBIEN DB: DB and bien user: mk_db: hstore extension: Fixed bug where need to use `CREATE EXTENSION hstore SCHEMA pg_catalog` instead of createlang, because hstore must be explicitly created in pg_catalog or else it will be created in the public schema instead, causing it to get deleted every time the public schema is reinstalled and cascading the delete to everything (including in other schemas) that uses hstore

sql_io.py: put_table(): Added special handling for functions with hstore params. Note that although _map() doesn't exist yet as a DB function, this code must be in place before _map() is created to avoid param type mismatch errors.

root Makefile: PostgreSQL: postgres-Linux: Changed plpython to plpython3 in order to install plpython3u

schemas/py_functions.sql: _date(): Removed features that require dateutil, which is not available under plpython3u. This includes removing the now-unused date string parameter.

mappings/VegCore-VegBIEN.csv: Removed _date/date, because _date using a string date argument is no longer supported under plpython3u (dateutil is missing). Note that PostgreSQL's own date parsing is sufficient for most dates, so this use of _date is not strictly necessary and removing it will improve import times.

schemas/py_functions.sql: Replaced xrange() with range() for plpython3u

root Makefile: Python: python-Linux: Also install python3, needed by plpython3u

schemas/py_functions.sql: Updated except clause syntax for PostgreSQL 9.1.6

schemas/*.sql: Updated for PostgreSQL 9.1.6, which has standard_conforming_strings = on (which affects \-escapes in string literals), escape_string_warning not explicitly set, and uses ALTER TABLE ONLY instead of ALTER TABLE

README.TXT: Removed step to manually run make_analytical_db, now that this is done automatically by import_all. Added separate instructions to remake the analytical DB.

import_all: Change to main directory make targets are run from. Use relative paths to bin/ commands, which is possible now that the current dir is set.

import_all: Create a background process that waits until the import is done and then runs make_analytical_db

Added waitpid

import_all: Documented that `wait %1` waits for asynchronous commands

root Makefile: VegBIEN DB: DB and bien user: mk_db: Also install hstore extension. Note that this is only supported by PostgreSQL 9.1+.

input.Makefile: Editing import: Updated queries for current schema

inputs/.geoscrub/geoscrub_cultivated/create.sql: Fixed bug where need to filter out NULL lat/longs because primary keys can't contain NULL values

schemas/py_functions.sql: Changed function languages to plpython3u to match the new installed version. Note that plpythonu is not available on Mac under PostgreSQL 9.1.6.

reinstall_all: Fixed bug where also need to include datasources starting with . such as .TNRS/, by using with_all's new $all option

with_all: Added $all option to also include datasources starting with . such as .TNRS/. This is necessary for reinstall_all, which needs to install all datasources.

root Makefile: PostgreSQL: $(pg_ctl-*): Fixed bug where need to pause for a few seconds after restarting PostgreSQL, to wait for the server to be ready to accept connections

root Makefile: Installation: uninstall: Removed inputs/uninstall because the DB will be uninstalled anyway, so the inputs don't need to be individually removed first

schemas/postgresql.Mac.conf: Added back unix_socket_directory setting, which is apparently still needed in PostgreSQL 9.1.6

root Makefile: PostgreSQL: postgres-Linux: Also install postgresql.conf

root Makefile: PostgreSQL: postgres-Darwin: Also install postgresql.Mac.conf

root Makefile: PostgreSQL: $(macUsePostgresLib): Factored out PostgreSQL dir to $(macPostgresDir)

schemas/postgresql.Mac.conf: Updated to PostgreSQL 9.1.6's postgresql.conf

root Makefile: Datasources: inputs/install: Fixed bug where need to `wait` after `. bin/reinstall_all` to wait for inputs to finish installing before installing the public schema. This is necessary because views in the public schema now have dependencies on some datasources, such as TNRS.

root Makefile: PostgreSQL: $(psqlAsAdmin): Use new $(asAdmin)

root Makefile: VegBIEN DB: Schemas: schemas/public/install: Use $(psqlNoSearchPath) instead of $(psqlAsBien) because the search_path is set by vegbien.sql

root Makefile: Datasources: Added inputs/install override which runs `. bin/reinstall_all` instead, in order to install all datasources simultaneously

root Makefile: Python: python-Darwin: Added instructions to install Python 3.2 (Python 2 comes with Mac OS X, but Python 3.2 is needed for plpython3u)

root Makefile: VegBIEN DB: DB and bien user: mk_db: Updated for PostgreSQL 9.1.6 on the Mac, which only provides plpython3u (Python 3)

root Makefile: VegBIEN DB: DB and bien user: mk_db: Updated for PostgreSQL 9.1.6, which requires the DB name to be specified on the command line instead of in the $PGDATABASE env var set by postgres_vegbien. Fixed bug where need to run createlang as postgres superuser, because plpythonu is an untrusted language (with unrestricted access to the entire DB).

root Makefile: PostgreSQL: postgres-Darwin: Updated for PostgreSQL 9.1.6, which requires some /usr/lib/ symlinks to be changed to newer versions installed in the PostgreSQL lib/ dir

input.Makefile: $(psqlAsBien), csv2db: Turn off the automatic search_path where needed, because when the input is installed, the schemas in it may not exist yet

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