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tests

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.