inputs/SpeciesLink/maps/DwC.specimens.csv: Mapped remaining fields

inputs/SpeciesLink/maps/DwC.specimens.csv: Mapped remaining fields

inputs/SpeciesLink/maps/src.specimens.csv: Fixed bug where prefixes had not been removed from fields, which prevented join mappings from being found for any of the fields

main Makefile: Added missing_joins to determine which input fields are missing join mappings

xml_func.py: SyntaxException: Inherit from exc.ExceptionWithCause so the traceback will be populated with the cause's traceback instead of the SyntaxException wrapper's traceback

Added inputs/UNCC/test with accepted test outputs

Added inputs/UNCC/maps

xml_func.py: _date: month: Convert month names to numbers before casting everything to int

xml_func.py: _date: Refactored to convert items to dict right away, and use iteritems() for later type conversion. This will enable month names to be converted before casting everything to int.

mappings/Makefile: Sort mappings/DwC.self.specimens.csv so that entries can more easily be found when using it as a DwC terms reference

Added inputs/UNCC

Added inputs/U/test with accepted test outputs

inputs/U/maps/DwC.specimens.csv: Mapped most of the remaining fields

input.Makefile: Clean up via maps when they change by subtracting the via format's self map from the via map (the comments column is ignored in determining which entries are redundant, and empty entries with a matching input column are also removed)

subtract: Fixed bug where entries were removed even if maps were not combinable and ignore was off

union: Fixed bug where combinable was not saved for use in deciding whether to add entries in map 1 that weren't already defined

inputs/U/maps: Set svn props

subtract: Also remove nonexplicit empty mappings whose input col is in map 1

maps.py: Added is_nonexplicit_empty_mapping()

subtract: Use new maps.combinable() to compare column headers, which allows more flexibility in combining maps

union: Use new maps.combinable()

maps.py: Added col_label() and combinable()

union: Use new strings.overlaps()

strings.py: Added overlaps()

vegbien.sql: Fixed sytnax error in taxonclass enum: missing comma at end of element

inputs/*/maps/DwC.specimens.csv: Ran through `cols *` to standardize CSV format to that generated by Python

cols: If column number of "*" given, get all columns

bin/subtract: If no compare columns given, compare on all columns instead of column 0

util.py: list_subset(): Support special idxs value None, which returns entire list

cat_csv: Added support for using - to cat stdin

Added inputs/U/maps

Added inputs/U

Put inputs/REMIB/src/remib_raw.0.header.specimens.txt under version control

Added inputs/REMIB/test with accepted test outputs

Added inputs/REMIB/maps

inputs/NCU-NCSC/maps/DwC.specimens.csv: Removed State->StateProvince mapping because that is now in mappings/DwC1-DwC2.specimens.csv

mappings/DwC1-DwC2.specimens.csv: Added common DwC1 fields that are not part of the official DwC1 schema

Added inputs/REMIB

bin/map: Deal with fields that may be in the dataset under more than one prefix by getting all fields and coalesce()ing them (e.g. SpeciesLink has dwcore* and darwin1* columns for the same DwC field)

util.py: Added coalesce()

xpath_func.py: process(): Fixed bug where XPath elem's other_branches were not also processed

row: Don't prepend header row because this feature prevents the program from being used on a pipeline. Sheets may be constructed in a pipeline if multiple segments need to be joined, e.g. with cat_csv.

Added row to get a row of a spreadsheet, preceded by the header row

bin programs: Fixed bug in Usage message where program name was not printed because unset variable $self was used instead of $0

xml_func.py: _nullIf: types_by_name: Use strings.ustr instead of str to support Unicode values

xml_func.py: _nullIf: If value not convertible, return it, because can't equal null. Refactored to store types by name in a dict instead of using if statements.

units.py: convert(): raise MissingUnitsException if quantity doesn't have units. MissingUnitsException: Take Quantity input instead of str.

inputs/NCU-NCSC/maps/DwC.specimens.csv: "Cultivated?": For clarity, use _map instead of _if to translate boolean to "cultivated". Translate "No" to "wild" (the opposite of "cultivated") to store an explicit not-cultivated as such.

inputs/NCU-NCSC/maps/DwC.specimens.csv: "Cultivated?": For clarity, use _map instead of _if to translate boolean to "cultivated". Translate "No" to "wild" (the opposite of "cultivated") to store an explicit not-cultivated as such.

xml_func.py: _map: empty map entry means None

xml_func.py: _avg: Support empty inputs by returning None. Moved _range after _rangeStart/_rangeEnd since it's less frequently used.

units.py: Restructured to use a Quantity object for the units-tagged value and conversion functions quantity2str() and str2quantity() to convert between that and a raw string. Added convert() with basic support for removing units and passing through matching units. xml_func.py: _units: Added "to" attr. VegBIEN mappings: Remove units using new _units "to" attr instead of temporary workaround in _units.

xml_func.py: _units: default units attr renamed to default to clarify that it's not the units you're converting to

xml_func.py: Added documentation labels to each section of XML functions

Moved units-related functions from format.py to new units.py

lib/*.py: Removed svn:executable property to turn execute bit off

vegbien.sql: growthform (and taxonclass) enum: Added options suggested by Michael Lee. Removed "woody". establishmentmeans_dwc (and taxonclass) enum: Reordered to match order of taxonoccurrence boolean fields, and to place each option next to its opposite. taxonclass enum: Moved "woody" to bottom because it's no longer part of growthform.

VegBIEN mappings: distance fields: Remove units

xml_func.py: _units: Allow value to be NULL

xml_func.py: _units: Use new format.cleanup_units() to do units parsing

format.py: Added clean_numeric(), str2int(), str2float(). Added units-related functions. Added documentation labels to each section.

Added filter_errors to filters `map` error messages

Renamed bin/errors_filter_* to filter_errors_* to sound more natural and to have a different prefix than error_stats so that both can easily be tab-completed at the command line

README.TXT: Testing: Added instructions for testing just mapping process, just map spreadsheet generation, and everything

root Makefile: Added test-all for most complete coverage. Removed extraneous ";" at the end of the prerequisites line of rules with a recipe.

mappings/Makefile: Use new ci_map to make DwC.cs-VegBIEN.specimens.csv case-insensitive

Added ci_map to make a map spreadsheet case-insensitive.

mappings: DwC: Generate case-insensitive map of DwC1 and DwC2 together, rather than just DwC2. DwC1-DwC2.specimens.csv: Make input columns lowercase so that case-insensitization will work properly.

inputs/SpeciesLink: Switched to using flat files instead of DB

inputs/MO: Switched to using flat files instead of DB

mappings: DwC: Generate case-insensitive map of DwC1 and DwC2 together, rather than just DwC2. DwC1-DwC2.specimens.csv: Make input columns lowercase so that case-insensitization will work properly.

input.Makefile: Mapping: Support multiple segments of a source table flat file. Use with_cat_csv if flat file segment(s) are available; otherwise use the input file in $+ or the input database, if any. Don't look for an explicit CSV header file because it can now be handled as the first segment if appropriately named.

Added with_cat_csv

with_cat: Added support for custom cat command in env var

cat_csv: Abort if output stream closed instead of exiting with an IOError

cat_csv: Ignore any duplicated headers instead of requiring each CSV to have a header identical to the first. Rewrote to pass the CSVs through as lines rather than parsing each row. Because the CSVs are not parsed, checked that all CSVs have the same dialect.

csvs.py: Added csv modifications to compare Dialect instances

util.py: Added classes_eq()

csvs.py: Added stream_info() to return NamedTuple {header_line, dialect} for later use in cat_csv. Changed reader_and_header() to use stream_info().

util.py: Added NamedTuple

csvs.py: reader_and_header(): Restrict delimiters to common delimiters so that e.g. letters are not considered delimiters just because they appear frequently

Renamed inputs/NYBG to inputs/NY to match herbarium code

Renamed inputs/UNC-NCSC to inputs/NCU-NCSC to match herbarium code

Renamed inputs/UArizona to inputs/ARIZ to match herbarium code

Regenerated inputs/MO/maps/src.join.specimens.csv

Renamed inputs/MOBOT to inputs/MO to match herbarium code

Regenerated vegbien.ERD exports

vegbien.sql: taxonoccurrence: Added cultivatedbasis

vegbien.sql: Moved all accessioncode fields to the bottom of their tables. vegbien.ERD.mwb: Adjusted lines to remove overlaps.

vegbien.sql: taxonoccurrence: Added iscultivated, isnative. Moved accessioncode to bottom.

vegbien.sql: Changed taxonoccurrence.growthform type to more specific growthform

vegbien.sql: Added growthform and establishmentmeans_dwc enums using values from taxonclass. Documented that taxonclass is growthform + establishmentmeans_dwc + some other values.

VegBIEN: Moved aggregateoccurrence.growthform to taxonoccurrence

Added inputs/UNC-NCSC/maps/src.join.specimens.csv

VegBIEN: Merged aggregateoccurrence.verbatimcollectorname and specimenreplicate.verbatimcollectorname into taxonoccurrence

xml_func.py: parse_range(): Handle negative numbers by treating them as not a range

Added inputs/UNC-NCSC/test with initial accepted test outputs

Added inputs/UNC-NCSC/maps

xml_func.py: _replace: Fixed bug where value entry was not unpacked

Added inputs/UNC-NCSC