SALVIAS verification: Updated to schema changes

input.Makefile: Fixed syntax error in verify %.ref target (outdated variable name)

input.Makefile: Halt psql commands on first error

vegbien.sql: Removed location.authorlocationcode because it's now stored in locationevent as an author-specific setting

vegbien.sql: locationevent: Redid unique constraints to avoid applying authorlocationcode-only duplicate elimination to subplots

SALVIAS mappings: Map SiteCode/plot_code to locationevent.authorlocationcode because locationevent is now the place to store author-specific plot information

SALVIAS mappings: Fixed PlotID mapping to go to locationevent.sourceaccessioncode

VegBIEN: Renamed locationevent.authoreventcode to authorlocationcode to reflect that datasources usually use an author-defined code for a plot rather than a plot event

vegbien.sql: locationevent: Redid unique constraints to handle datasources that treat the authoreventcode as an authorlocationcode. Eventually, authoreventcode will be renamed to authorlocationcode.

vegbien.sql: locationevent: Redid unique constraints to work properly for all fully-specified combinations of keys

VegBIEN mappings: Mapped datasource name to new project.datasource. Fixes project duplicate elimination.

vegbien.sql: Renamed project.reference_id to datasource_id and pointed it to party, to match locationevent, etc.

VegBIEN mappings: Mapped current lat/long to centerlat/long as well so location duplicate elimination will work properly

xpath.py: Added support for common subpath after split path's {}

sql.py: put(): When encountering a DuplicateKeyException, use dict_subset_right_join to fill in explicit NULL values for columns which don't have data. This causes the database to use the UNIQUE constraint's index to look up the record, instead of relying on individual column indexes for the columns that did have data, which may or may not be available.

util.py: Added DefaultDict to wrap collections.defaultdict with a simple value passed in the constructor, defaulting to None. Added dict_subset_right_join() to fill in None for subset keys that don't exist.

vegbien.sql: Added method and plotmethod UNIQUE indexes

vegbien.ERD.mwb: Removed embargo table from ERD because its functionality is provided in location.confidentialitystatus,confidentialityreason

Regenerated vegbien.ERD exports

vegbien.sql: Moved locationevent method fields to plotmethod and method. Added comments to method/plotmethod fields, as provided by Michael Lee.

VegX-VegBIEN mapping: Mapped locationevent.methodnarrative to new plotmethod table

Regenerated vegbien.ERD exports

VegX-VegBIEN mapping: Map sourceaccessioncode and voucher (catalognumber_dwc) to correct place. SALVIAS mappings: Map SourceVoucher as an alternative to coll_number.

vegbien.sql: Removed VegBank-internal tables (including user account tables) because they do not belong in the ecological database. Any web interface should store user account information, cached queries, etc. in a separate interface-specific database.

VegX-VegBIEN mapping: Mapped stem tags to new stemtag table

vegbien.sql: Renamed planttag to stemtag and made it a child of stemobservation. Removed trait table from ERD because it's not used for the purpose we want to use traits for.

vegbien.sql: Removed no longer used location.reference_id. Datasource scoping is now done on locationevent instead, so that locations can be shared across datasources that refer to the same plot or point.

VegX-VegBIEN mapping: Map datasource name (/_ignore/inLabel) to new locationevent.datasource instead of location.reference

vegbien.sql: Added locationevent.datasource_id

vegbien.sql: locationevent: Removed VegBank-internal interp_* fields

VegBIEN: Renamed specimenreplicate.reference_id to datasource_id and pointed it to party instead of reference, since party is better optimized for storing names

DwC mappings: Mapped datasource name to specimenreplicate.reference instead of location.reference

DwC mappings: Mapped specimen description via fieldNotes instead of custom bien.specimenDescription field

VegBIEN: Moved specimenreplicate.verbatimcollectorname to taxonoccurrence since it can also apply to aggregateoccurrences. Removed no longer needed taxonoccurrence fields which are now in taxondetermination.

SALVIAS mappings: Mapped habit to growthForm (user-defined field) instead of habit

DwC-VegBIEN mapping: Convert latitude/longitude values of exactly zero to NULL

xml_func.py: Added _nullIf

util.py: Fixed cast() to not cast a subclass to a superclass (which doesn't make sense in a dynamically-typed language). Added none_if().

util.py: Removed locale import since it's no longer used by util

NYBG-DwC mappings: Map Vegetation to habitat (merged with Habitat). DwC-VegBIEN mapping: Removed remaining mappings to plantobservation.

DwC-VegBIEN mapping: Added datasource name to location.reference using /_ignore/inLabel

profiling.py: Support Python before 2.7 by using new dates.total_seconds(). Also use dates.now() to ensure datetimes always have a timezone.

dates.py: Fixed timestamp() to deal with microseconds correctly by adding them after time.mktime()

dates.py: Deal properly with different timezones by using external dateutil package. Added total_seconds() to replace datetime.timedelta.total_seconds() on Python before 2.7.

vegbien.sql: *method tables: Added table comments

VegX-VegBIEN mapping: Reordered 2-step-only mappings that use /_ignore/inLabel so they run at the same time as other mappings that set the field that uses /_ignore/inLabel. This fixes almost all of the failing 2-step tests.

Regenerated vegbien.ERD exports

vegbien.sql: method: Added lengthunits field

vegbien.sql: Changed types of numerical plotmethod fields to double precision

vegbien.sql: method, plotmethod: Added comments to fields

vegbien.ERD.mwb: Adjusted lines

vegbien.sql: Added plotmethod. locationevent points to plotmethod instead of directly to method

vegbien.sql: Point to covermethod from method instead of locationevent

vegbien.sql: Removed no longer needed sizeclass table (whose fields are now in method)

vegbien.sql: Replaced stratumtype, stratummethod with method

vegbien.sql: Attach method to aggregateoccurrence instead of taxonoccurrence

vegbien.sql: Removed methodtrait* tables and added first-class method attributes as first-class fields of method. Removed *method tables from the ERD that will be replaced by method.

vegbien.sql: Removed location.dsgpoly because it is now locationdetermination.footprintgeometry_dwc

VegBIEN mappings: Remap to new locationdetermination fields

VegBIEN: Renamed location.reallatitude,reallongitude to centerlatitude,centerlongitude to reflect that it's now a value calculated from the centroid of the current locationdetermination

vegbien.sql: locationdetermination: Reordered fields

vegbien.sql: locationdetermination.coordsaccuracy: Added comment with units

vegbien.sql: locationdetermination: Added determination status columns from taxondetermination

vegbien.sql: locationdetermination: Added coordinates-related fields

VegX-VegBIEN mapping: Include the datasource name (now provided by map in /_ignore/inLabel) in the appropriate places in both VegX and VegBIEN

bin/map: Removed metadata values feature since the syntax used was causing problems with mappings starting with a ":", and metadata can instead be stored as attributes of the primary key's mapping

xml_dom.py: Fixed bug in parent() where it didn't account for NodeParentIter's first element returned being the current node, not its parent. Refactored parent() to use parentNode directly, and NodeParentIter to use parent(), instead of the other way around.

xml_dom.py: Fixed bug in parent() where incorrect variable name was used

VegX-VegBIEN mapping: Use the input data source's label (e.g. SALVIAS) everywhere a reference is needed

bin/map: Store the input data source's label (e.g. SALVIAS) in the output XML tree for use by references in the mappings

xpath.py: get(): Fixed bug where it would try to create a node named . or .. if . or .. didn't have matching attributes. Now it will just reuse the current or parent node, but create any needed attrs if create is True.

util.py: Added list_eq_is() to compare two lists using is

xpath.py: Don't allow rooted attributes (doesn't make sense), in case someone tries to do elem[/rooted_attr]

bin/map: Moved root.clear() into separate function prep_root() that can be called whenever needed

xpath.py: Added get() support for references (different from pointers) to dynamically set the value of an attribute

util.py: Added list_get()

util.py: Added is_list()

bin/map: Use var doc0_root for quick reference to doc0's root

xpath.py: get(): Go to root when empty element is encountered at the beginning of an XPath. Added allow_rooted parameter to turn off this functionality when XPaths with a leading slash should not be considered rooted.

xpath.py: Don't consider a path starting with "." to be rooted. Do this by not automatically translating an empty path name to ".".

xpath.py: Added is_rooted()

xpath.py: Added elem_is_empty()

xpath.py: Added documentation labels to each section

xpath.py: Added support for getting the parent node when encountering ".."

xml_dom.py: Added parent() to get parent node without recursing past the root node to the document object. Documented that NodeParentIter incorporates this sanity check.

xpath.py: get(): Renamed parent to root to better reflect that it's the starting point for the search. Calling it parent will later be confusing when we want to get the parent node using "..".

xpath.py: Added parser support for attribute values that are references to another part of the XML tree

xml_func.py: Fixed module description comment to reflect that not all XML funcs generate text

xml_func.py: Refactored to add funcs to the module funcs variable as they are defined. Renamed defined functions to the name of the corresponding XML function.

xml_func.py: Added _ignore func to "comment out" an XML subtree

input.Makefile: Fixed error message when no DB file found so that it doesn't incorrectly imply that PostgreSQL inputs are supported

input.Makefile: Fixed error message when no DB file found so that it doesn't incorrectly imply that PostgreSQL inputs are supported

input.Makefile: Don't run tests in verbose mode because the run time stats, etc. are not relevant

bin/map: Only print error/run time stats in verbose mode. input.Makefile: Run import in verbose mode so that error/run time stats are still printed.

Moved value to string conversion functions infrom util.py to new module format.py

exc.py, profiling.py: Use util.int2str() to print # iters with thousands separators

util.py: Added int2str()

bin/map: Document that the exit status is the # of errors in the import, up to the maximum exit status

exc.py: Generalize ExTracker to not just print the # of errors at exit. Instead, provide an exit() method that the ExTracker creator can call at exit to set the exit status to the # of errors. This fixes the Python bug where a benign error message was printed if SystemExit was raised in an atexit function.

bin/map: Set ExPercentTracker's iter_text. Start ExPercentTracker after input processing, because errors in command line options should just end the program and don't need to be tracked.