mappings/Makefile: Run simplify_xpath on VegX-VegBIEN.organisms.csv

simplify_xpath: Be case sensitive to handle VegX correctly

VegX-VegBIEN mapping: Avoid using a dummy taxondetermination with role=collector

VegX-VegBIEN mapping: Map stem count to new stemcount field

VegX-VegBIEN mapping: Take advantage of aggregateoccurrence.count being optional

vegbien.sql: Made aggregateoccurrence.count to handle individuals data (for which count should be dynamically determined from # individual plants inside the aggregateoccurrence)

NYBG-VegBIEN mapping: Don't map dummy values to locationcode, etc. (e.g. in specimens data) because these tables are no longer required

vegbien.sql: Made several pointers to parent elements optional to deal with specimens data that might not have a location, etc.

vegbien.sql: Added taxondetermination UNIQUE constraint

VegX-VegBIEN mapping: Took advantage of location.confidentialitystatus being optional

VegX-VegBIEN mapping: Took advantage of userdefined.userdefinedtype being optional

vegbien.sql: Gave userdefined.userdefinedtype a default value

VegX-VegBIEN mappings: Took advantage of plantconcept.reference_id becoming optional

vegbien.sql: Made plantconcept.reference_id optional. Merge plantconcepts with no reference_id when eliminating duplicates.

PostgreSQL-MySQL.csv: Deal with all non-NOT NULL timestamp fields

vegbien.sql: Removed confusing plantconcept.plantname field since we are using plantname.plantname instead

VegBIEN: Renamed aux_role to role

VegX-VegBIEN mappings: Took advantage of several fields becoming optional

VegX-VegBIEN mappings: Took advantage of several fields becoming optional

Regenerated vegbien.ERD exports

vegbien.sql: taxonbinmethod points to stratumtype instead of stratum because stratumtype is a method table, but stratum is a measurements table. stratum does not point directly to stratummethod because it points to it via stratumtype.

vegbien.sql: Made taxondetermination.determinationdate optional because some determinations might not have a date

Regenerated vegbien.ERD exports

vegbien.sql: Added specimen.authorspecimencode

Adjusted vegbien.ERD.mwb

Regenerated vegbien.ERD exports

VegBIEN: Renamed sourceaccessionnumber to sourceaccessioncode to show that they are the data source's analog of accessioncode. Added sourceaccessioncode to all applicable tables because this is the database pkey, which is distinct from any author*code applied by the collector.

vegbien.sql: Changed taxonbinmethod_keys to UNIQUE INDEX to take advantage of COALESCE for dealing with NULL values

vegbien.sql: Renamed taxonbin to taxonbinmethod to reflect that it does not contain actual organisms (those go in aggregateoccurrence), but rather defined a method of aggregating organisms

vegbien.sql: Removed taxonbin.count because that belongs in aggregateoccurrence and taxonbin is more similar to a sampling method. Added taxonbin UNIQUE constraint.

vegbien.sql: Do location duplicate elimination independently on code or lat/long, allowing duplicate entries with NULLs to exist when a location is incompletely specified

vegbien.sql: Require location to have either an authorlocationcode or a lat/long. Distinguish between regular and subplots in UNIQUE constraint.

vegbien.sql: Renamed location.latitude and longitude to publiclatitude, publiclongitude to reflect that they are not the actual lat/long. Switched to requiring reallatitude/reallongitude.

Added inputs/TurboVeg

vegbien.ERD.mwb: Deal with MySQL assuming that a timestamp field is NOT NULL

PostgreSQL-MySQL.csv: Deal with MySQL assuming that a timestamp field is NOT NULL

vegbien.sql: Made specimen.taxonoccurrence_id required

vegbien.sql: Made several fields optional, adding defaults where needed

PostgreSQL-MySQL.csv: Deal with PostgreSQL-style :: casts

NYBG mappings: Add mapping for CollectorNumber to specimen.collectornumber_dwc

vegbien.sql: Added specimen.collectornumber_dwc

VegBIEN: Renamed sourceid to author*code

VegBIEN: Renamed sourceid to author*code

mappings: Map ScientificNameAuthor to plantconcept with rank author

vegbien.sql: Removed sizeclass.*precision fields

vegbien.sql: Added count field to taxonBin

VegBIEN: Renamed place to locationplace

vegbien.sql.make: Exclude 'CREATE OR REPLACE PROCEDURAL LANGUAGE plpgsql' to avoid restore errors

repl: When matching words, treat _ as word boundary and ignore case.

VegBIEN: Renamed individualplant.height to overallheight

Regenerated vegbien.ERD exports

PostgreSQL-MySQL.csv: Convert double quotes to backticks (`)

Regenerated vegbien.ERD exports

vegbien.for_ERD.sql: Fixed syntax error in stratum table

Regenerated vegbien.ERD exports

vegbien.sql: Renamed sizeclass.*accuracy to *precision to reflect intended purpose

vegbien.sql: Added stem.diameteraccuracy

vegbien.sql: Removed taxonoccurrence.currentdetermination_id and originaldetermination_id because it's not possible to create a two-way pointer when the child-to-parent pointer is required (chicken-and-egg problem)

README.TXT: Added make empty_db

vegbien.sql: Added taxonoccurrence.currentdetermination_id and originaldetermination_id

vegbien.ERD.mwb: Added stratum and place tables

Added vegbien.ERD.png

Added vegbien.ERD.svg

Added vegbien.ERD.pdf

Added vegbien ERD

Ignore *.bak in schemas

VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant

vegbien.sql: Made voucher fields NOT NULL

vegbien.sql: Added voucher table

VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant

VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant

Create schemas/vegbien.for_wiki.sql from schemas/vegbien.for_ERD.sql

Added lib/ERD-wiki.csv to convert ERD SQL to human-readable wiki format

schemas/vegbien.for_ERD.sql: Removed VegBank-internal fields from taxonoccurrence

Removed no longer needed schemas/vegbien.my.sql

PostgreSQL-MySQL.csv: Use \g<0> instead of \0 in replacements because \0 not supported. Replace fulltext with fulltext__ (note fulltext_ doesn't work).

Added schemas/vegbien.for_ERD.sql and generated MySQL

Regenerated schemas/vegbien.for_ERD.sql

PostgreSQL-MySQL.csv: Deal with serial NOT NULL fields

Generate MySQL DDL schemas/vegbien.my.sql from vegbien.sql

Added repl spreadsheet to map PostgreSQL DDL to MySQL

Ignore src subdirectories in inputs

VegBIEN: Use stem instead of individualplant to store diameter/dbh

vegbien.sql: Removed no longer needed taxondetermination.plantname_id

VegBIEN: Made taxondetermination.plantconcept_id required and plantname_id optional

vegbien.sql: Added specimen.taxonoccurrence_id fkey

vegbien.sql: Removed no longer needed taxondetermination.individualplant_id, specimen_id fields

VegBIEN: Renamed plot to location to reflect that a location can also be used for specimens

vegbien.sql: Added individualplant.stemcount

vegbien.sql: Added accessioncode fields to existing, modified tables

vegbien.sql: Added accessioncode fields to new tables

vegbien.sql: Removed no longer needed individualplant.taxonarea

VegBIEN: Moved taxondetermination.sourceaccessionnumber and museum_id to specimen

vegbien.sql: Split taxondetermination UNIQUE CONSTRAINT into one constraint for each main key (taxonoccurrence_id, specimen_id, individualplant_id) to deal with Postgres treating a row with NULL in any of those columns as distinct. Added CHECK constraint to require one of taxonoccurrence_id, specimen_id, individualplant_id to be NOT NULL.

VegBIEN: Renamed museumaccessionnumber to sourceaccessionnumber

VegBIEN: Renamed authorcode to sourceid

vegbien.sql: Updated sizeclass to use ranges for parameters and remove taxonarea

input.Makefile: Fixed verify by making %.out: % rule use %.make instead

input.Makefile: Moved verifications into one set of verify.* files

input.Makefile: All tests are run in the same transaction, with output to test.out