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

bin/map: Added support for processing multiple map_paths at once in the same transaction

SALVIAS organisms mapping: Removed redundant PlotCode mapping because the association to plotevent is done with PlotID

bin/map: Started adding support for multiple map_paths, all run in the same db transaction

Filled in SALVIAS stems mappings. make test2's stems test fails because we don't wrap the import transaction around all the tests so that organisms are already in the database when stems are imported.

mappings/Makefile: Corrected stemobservation to stem

Use baseDistance/complexUserDefined/method to distinguish between different dbhs in VegX

VegX mappings: Use baseDistance/value instead of baseDistance so we can later use complexUserDefined to distinguish between different types of dbh

VegX-VegBIEN.organisms.csv: Added initial stems mappings

mappings/Makefile: Updated VegX-VegBIEN.stems.csv input/output roots

ch_root: Deal with roots followed by something other than \b

input.Makefile: Remove *.out in new verify and test subdirs

Moved inputs files into subdirs for maps, verify, and test operations

vegbien.sql: Removed taxondetermination.collector_id because that's now in specimen

VegBIEN: Map to specimen.collector_id instead of taxondetermination

vegbien.sql: Added specimen.collector_id column

vegbien.sql: Changed taxondetermination.stem_id to individualplant_id

vegbien.sql: Removed taxondetermination columns that have been moved to specimen

VegBIEN: Merged specimen.collectionnumber and catalognumber_dwc fields. Removed NOT NULL constraints on several specimen columns because not all specimens have all identifiers. Mapped to new specimen fields.

VegX-VegBIEN mapping: Map collectiondate to specimen table

vegbien.sql: Added specimen.collectionnumber and collectiondate fields

Updated README.TXT to reflect new make targets

vegbien.sql: Added sizeclass columns

VegBIEN: Removed stem* prefix from stem measurements because it's redundant and because these same field names were reused in non-stem tables

VegBIEN: Renamed stemobservation to stem

vegbien.sql: Added comments to renamed tables specifying VegBank equivalent

vegbien.sql: Added comments to new tables

vegbien.sql: Removed r# prefix from foreign key constraints

vegbien.sql: Added plot.namedplace_id for theplots which are identified by a namedplace rather than lat/long or name

vegbien.sql: Made plot.authorcode optional as not all plots have names

vegbien.sql: Added _dwc to specimen columns that are from DwC

vegbien.sql: Added UNIQUE constraint for specimen table. Made catalognumber required so that all specimens can be uniquely identified.

vegbien.sql: Made specimen.individualplant_id optional because specimens are not required to have a corresponding plot event (which all individualplants must have)

VegBIEN-VegBank.csv: Updated to reflect renames

vegbien.sql: Renamed specimen.code to collectioncode to match DwC term

vegbien.sql: Added sizeclass table

vegbien.sql: Renamed collection to specimen to reflect that it's for a single collection specimen

VegBIEN: Renamed collectiveobservation to aggregateoccurrence to reflect VegX usage of aggregate and the new taxonoccurrence table