obis-qc

Install

pip install git+https://github.com/iobis/isodateparser.git
pip install git+https://github.com/iobis/pyxylookup.git
pip install git+https://github.com/iobis/pyworms.git
python setup.py install

Run tests

nosetests --with-coverage --cover-package=obisqc --cover-html

Quality checks

The following checks are performed on each occurrence record in order to add quality flags, tag as absence data, or drop records from the main index:

Check	Fields	Flags	Absence	Dropped	Vandepitte et al. flag number
occurrenceStatus should be present.	occurrenceStatus
occurrenceStatus should be absent or present.	occurrenceStatus		x
If individualCount equals 0, record is absence.	individualCount		x
eventDate should be present.	eventDate				7, 11, 12, 13
eventDate should conform to ISO 8601.	eventDate
eventDate should not be in the future.	eventDate	date_in_future
eventDate should be later than the set minimum date.	eventDate	date_before_min
decimalLongitude and decimalLatitude should be present.	decimalLongitude, decimalLatitude	no_coord		x
decimalLatitude and decimalLongitude should not be zero.	decimalLongitude, decimalLatitude	zero_coord		x	4
decimalLatitude and decimalLongitude should be within range.	decimalLongitude, decimalLatitude	lon_out_of_range, lat_out_of_range, no_coord		x	5
coordinateUncertaintyInMeters should be present.	coordinateUncertaintyInMeters
minimumDepthInMeters and maximumDepthInMeters should be present.	minimumDepthInMeters, maximumDepthInMeters
minimumDepthInMeters and maximumDepthInMeters should be within range.	minimumDepthInMeters, maximumDepthInMeters	depth_out_of_range
minimumDepthInMeters and maximumDepthInMeters should be less than or equal to the bathymetric depth.	minimumDepthInMeters, maximumDepthInMeters	depth_exceeds_bath			19
Is the occurrence located on land?	decimalLongitude, decimalLatitude	on_land			6
scientificName should be present.	scientificName
scientificNameID should be present.	scientificNameID
scientificNameID should be valid WoRMS LSID.	scientificNameID				2
Taxon should unambiguously match with WoRMS.	scientificName, scientificNameID	no_match		x
An accepted name should exist in WoRMS.	scientificName, scientificNameID	no_accepted_name
Taxon should not be exclusively freshwater or terrestrial according to WoRMS.	scientificName, scientificNameID	not_marine, marine_unsure		in case of not_marine

Vandepitte et al. flags not implemented: 3, 9, 14, 15, 16, 10, 17, 21-30.