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

VegBIEN: Renamed stemobservation.stemcode to authorcode

vegbien.sql: Renamed individualplant.code to authorcode

sql.py: Reordered get() args to match put()

db_xml.py: Use new sql.put() which only eliminates duplicates based on database UNIQUE constraints

sql.py: Added new function put() and changed get() to use it

sql.py: Fixed raising of NullValueException to pass array of columns rather than single column

vegbien.sql: Added UNIQUE constraints to tables used in the mapping so that duplicates are eliminated by the database

sql.py: ExceptionWithColumn now stores multiple columns so that they can all be used in DuplicateKeyExceptions

util.py: Fixed dict_subset() to work correctly when a key does not exist

util.py: Added dict_subset()

sql.py: Use constraint_cols() to determine DuplicateKeyException column in try_insert()

sql.py: Added constraint_cols() to get columns of a constraint for use in determining the columns for a DuplicateKeyException

db_xml.py: Map empty fields to None instead of ignoring them, to ensure that an existing row with a value in that field is not used in the duplicate elimination

bin/map: Use db_xml.put()'s new on_error handler

db_xml.py: put(): Added on_error handler. Reordered arguments according to how often they are likely to be used.

bin/map: Print # input rows processed

VegX-VegBIEN mapping: Merge different sources of plot elevation

vegbien.sql: Added individualplant.code field

xml_func.py: Expand XML funcs in XML func args

xml_dom.py: In NodeTextEntryIter, return non-text children as-is instead of ignoring them so that XML functions can use them

xml_dom.py: Improved readability by separating into sections

db_xml.py: Ignore only fields that are actually empty (rather than just not having element children), as a field containing anything other than a comment should be flagged as invalid input

xml_dom.py: Changed is_empty() to consider nodes with only comments to be empty

bin/map: Add input row to exceptions

db_xml.py: Ignore empty fields. Fixes bug where a field that's not text but has no Element children will be treated as a table, and an error is triggered because the corresponding table does not exist in the database.

xml_dom.py: Added has_elems() to check if node has Element children

bin/map: Use xml_func.process()'s new on_error error handler. Add row to database errors and xml_func.SyntaxExceptions.

xml_func.py: Changed formatting of comment that node with syntax errors is replaced with so that it starts on its own line

xml_func.py: Use on_error exception handler to allow caller to print exceptions instead of raising them

db_xml.py: Add node to any database exceptions generated in put()

exc.py: Added raise_() wrapper for raise statement

Ignore .~* (lock files generated by OpenOffice.org) in inputs

inputs/SALVIAS: Added stems map

bin/map: Handle empty rows for db output

mappings: Use stemParent instead of stemOrganism to identify stems so that it's clear that the stemParent is an individualOrganismObservation, not an individualOrganism

input.Makefile: Include VegX maps not in tablesSort

mappings/Makefile: Generate initial VegX-VegBIEN.stems.csv

mappings/Makefile: Cleaned up in preparation for adding rule to generate VegX-VegBIEN.stems.csv

bin/map: Continue with database insertion even if a row had XML func syntax errors, because these errors have been fixed by removing the offending function node

xml_func.py: Remove function nodes with syntax errors to prevent them from causing DatabaseErrors later

xml_dom.py: Added remove() function to remove a node

bin/map: Track Exceptions with ExTracker

exc.py: Added ExTracker to track printed (suppressed) Exceptions and exit with nonzero status if any were encountered

bin/map: Parse each output XPath at the beginning so XPath syntax errors are detected right away

vegbien.sql: Reran renames to capture cases where a name is in the middle of an identifier

vegbien.sql: Use character varying(255) instead of text or character varying in new tables and columns

input.Makefile: Print Postgres NULL as NULL instead of empty string to match MySQL output

VegX-VegBIEN mapping: Fixed syntax error in mapping

vegbien.sql: Added trait table

vegbien.sql: Added columns to stemobservation

vegbien.sql: Renamed collectiveobservation.stratum_id to taxonbin_id

vegbien.sql: Added some DarwinCore attributes to collection table

Makefiles: Added remake target to run clean and all

vegbien.sql: Added taxondetermination.collection_id column

VegBIEN: Made taxondetermination.plantname_id required

vegbien.sql: Made taxondetermination.plantconcept_id optional

VegBIEN: Renamed author*code to authorcode

Makefiles: Added empty rules for targets without a rule so that these rules wouldn't trigger the recursive subdir invocation for the default target

VegX-VegBIEN mapping: Convereted all database names to lowercase to correspond to their case in the database

Makefiles: Added empty Makefile target so that Makefiles are not included in the targets recursively run on subdirs

input.Makefile: Dependencies in other directories are included as prerequisistes. Use tablesSort variable instead of sort order prefix to order tables.

Makefile: Added default target that recursed into subdirs with Makefiles. Used default target for all and clean.

Regenerated inputs/SALVIAS/map.VegBIEN.0.plots.csv

Removed scripts symlink because it was causing Makefile recursion issues

Makefile: Take advantage of new inputs/Makefile

Added inputs/Makefile to run input targets recursively on each input

Makefile: Run inputs-* targets for all and clean

input.Makefile: all doesn't run import. import runs verify.

vegbien.sql: Set all FOREIGN KEY constraints to ON UPDATE CASCADE ON DELETE CASCADE

SALVIAS mappings: use PlotID as authorObsCode to link plot observations and organisms correctly for organisms without a PlotCode

SALVIAS mappings: use PlotID as authorObsCode to link plot observations and organisms correctly for organisms without a PlotCode

input.Makefile: Fixed bug in verify's diff rule

Added CTFS input

Makefile: Generate error when trying to run subMake on a directory with no Makefile

input.Makefile: Tests use bin/map's new new test mode

bin/map: Added test mode that empties the database before doing anything

sql.py: Added functions to truncate tables, list all tables, and empty a database

Accepted new SALVIAS test outputs

Makefile: Print Finished message after running test2 (inputs tests)

Accepted test outputs for SALVIAS