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