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[BDRSPS-918] First stab adding coordinateUncertaintyInMeters #290

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merged 12 commits into from
Nov 6, 2024
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[BDRSPS-918] First stab adding coordinateUncertaintyInMeters #290

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8916617
[BDRSPS-918] First stab at ticket
chungvl Oct 30, 2024
65efd42
[BDRSPS-918] First go, sanity check-in
chungvl Oct 31, 2024
8605671
[BDRSPS-918]
chungvl Oct 31, 2024
1132a71
[BDRSPS-918] Added `coordinateUncertaintyInMeters`
chungvl Oct 31, 2024
5f5d813
[BDRSPS-918] Added `coordinateUncertaintyInMeters`
chungvl Oct 31, 2024
30dd667
Merge branch 'main' of github.com:gaiaresources/abis-mapping into BDR…
chungvl Oct 31, 2024
7519c4c
[BDRSPS-913]
chungvl Nov 5, 2024
12b0644
[BDRSPS-918] Rolled back changes to survey metadata
chungvl Nov 5, 2024
f7d5dbd
Merge branch 'main' of github.com:gaiaresources/abis-mapping into BDR…
chungvl Nov 5, 2024
fdda36a
[BDRSPS-913] Updated unit tests affected
chungvl Nov 5, 2024
f084c5a
[BDRSPS-918] Response to MR feedback
chungvl Nov 6, 2024
ed49966
[BDRSPS-918] Reformat
chungvl Nov 6, 2024
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21 changes: 12 additions & 9 deletions ...ates/incidental_occurrence_data_v3/examples/margaret_river_flora/margaret_river_flora.ttl
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Original file line number Diff line number Diff line change
Expand Up @@ -1509,7 +1509,6 @@
<http://createme.org/sampling/field/14> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
geo:hasGeometry _:N7b30d47b6a23a645ada08e200000001a ;
geo:hasMetricSpatialAccuracy 2e+01 ;
rdfs:comment "field-sampling" ;
time:hasTime [ a time:Instant ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
Expand All @@ -1523,7 +1522,6 @@
<http://createme.org/sampling/field/15> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
geo:hasGeometry _:N7b30d47b6a23a645ada08e200000001c ;
geo:hasMetricSpatialAccuracy 5e+01 ;
rdfs:comment "field-sampling" ;
time:hasTime [ a time:Instant ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
Expand All @@ -1537,7 +1535,6 @@
<http://createme.org/sampling/field/16> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
geo:hasGeometry _:N7b30d47b6a23a645ada08e200000001e ;
geo:hasMetricSpatialAccuracy 3e+01 ;
rdfs:comment "field-sampling" ;
time:hasTime [ a time:Instant ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
Expand Down Expand Up @@ -2080,23 +2077,26 @@

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.86 115.02)"^^geo:wktLiteral ] ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.86 115.02)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 2e+01 ] ;
rdf:object _:N7b30d47b6a23a645ada08e200000001a ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/field/14> ;
rdfs:comment "supplied as" .

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ] ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 5e+01 ] ;
rdf:object _:N7b30d47b6a23a645ada08e200000001c ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/field/15> ;
rdfs:comment "supplied as" .

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ] ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 3e+01 ] ;
rdf:object _:N7b30d47b6a23a645ada08e200000001e ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/field/16> ;
Expand Down Expand Up @@ -2182,13 +2182,16 @@ _:N7b30d47b6a23a645ada08e2000000018 a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.86 115.02)"^^geo:wktLiteral .

_:N7b30d47b6a23a645ada08e200000001a a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.86 115.02)"^^geo:wktLiteral .
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.86 115.02)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 2e+01 .

_:N7b30d47b6a23a645ada08e200000001c a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral .
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 5e+01 .

_:N7b30d47b6a23a645ada08e200000001e a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral .
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 3e+01 .

_:Nfc9ba55a50d500211c02e20000000001 a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.86 115.02)"^^geo:wktLiteral ;
Expand Down
13 changes: 7 additions & 6 deletions abis_mapping/templates/incidental_occurrence_data_v3/mapping.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1441,13 +1441,20 @@ def add_sampling_field(
graph.add((geometry_node, a, utils.namespaces.GEO.Geometry))
graph.add((geometry_node, utils.namespaces.GEO.asWKT, geometry.to_transformed_crs_rdf_literal()))

spatial_accuracy = row["coordinateUncertaintyInMeters"]
accuracy = None
if spatial_accuracy is not None:
accuracy = rdflib.Literal(spatial_accuracy, datatype=rdflib.XSD.double)
graph.add((geometry_node, utils.namespaces.GEO.hasMetricSpatialAccuracy, accuracy))

# Add 'supplied as' geometry
self.add_geometry_supplied_as(
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subj=uri,
pred=utils.namespaces.GEO.hasGeometry,
obj=geometry_node,
geom=geometry,
graph=graph,
spatial_accuracy=accuracy,
)

# Add temporal members
Expand Down Expand Up @@ -1476,12 +1483,6 @@ def add_sampling_field(
# Add Location Description
graph.add((uri, utils.namespaces.TERN.locationDescription, rdflib.Literal(row["locality"])))

# Check for coordinateUncertaintyInMeters
if row["coordinateUncertaintyInMeters"]:
# Add Spatial Accuracy
accuracy = rdflib.Literal(row["coordinateUncertaintyInMeters"], datatype=rdflib.XSD.double)
graph.add((uri, utils.namespaces.GEO.hasMetricSpatialAccuracy, accuracy))

def add_provider_record_id_agent(
self,
uri: rdflib.URIRef,
Expand Down
21 changes: 12 additions & 9 deletions ...emplates/survey_occurrence_data_v2/examples/margaret_river_flora/margaret_river_flora.ttl
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1509,7 +1509,6 @@
<http://createme.org/sampling/field/14> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Systematic-Survey-Occurrence-Dataset> ;
geo:hasGeometry _:N80c91623373a353a57a815210000001b ;
geo:hasMetricSpatialAccuracy 2e+01 ;
rdfs:comment "field-sampling" ;
time:hasTime [ a time:Instant ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
Expand All @@ -1523,7 +1522,6 @@
<http://createme.org/sampling/field/15> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Systematic-Survey-Occurrence-Dataset> ;
geo:hasGeometry _:N80c91623373a353a57a815210000001d ;
geo:hasMetricSpatialAccuracy 5e+01 ;
rdfs:comment "field-sampling" ;
time:hasTime [ a time:Instant ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
Expand All @@ -1539,7 +1537,6 @@
<http://createme.org/sampling/field/16> a tern:Sampling ;
void:inDataset <http://createme.org/dataset/Example-Systematic-Survey-Occurrence-Dataset> ;
geo:hasGeometry _:N80c91623373a353a57a815210000001f ;
geo:hasMetricSpatialAccuracy 3e+01 ;
rdfs:comment "field-sampling" ;
time:hasTime [ a time:Instant ;
time:inXSDDate "2019-09-26"^^xsd:date ] ;
Expand Down Expand Up @@ -2123,23 +2120,26 @@

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.86 115.02)"^^geo:wktLiteral ] ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.86 115.02)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 2e+01 ] ;
rdf:object _:N80c91623373a353a57a815210000001b ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/field/14> ;
rdfs:comment "supplied as" .

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ] ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 5e+01 ] ;
rdf:object _:N80c91623373a353a57a815210000001d ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/field/15> ;
rdfs:comment "supplied as" .

[] a rdf:Statement ;
geo:hasGeometry [ a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ] ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/4326> POINT (-33.8 115.21)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 3e+01 ] ;
rdf:object _:N80c91623373a353a57a815210000001f ;
rdf:predicate geo:hasGeometry ;
rdf:subject <http://createme.org/sampling/field/16> ;
Expand Down Expand Up @@ -2201,13 +2201,16 @@ _:N80c91623373a353a57a8152100000019 a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.86 115.02)"^^geo:wktLiteral .

_:N80c91623373a353a57a815210000001b a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.86 115.02)"^^geo:wktLiteral .
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.86 115.02)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 2e+01 .

_:N80c91623373a353a57a815210000001d a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral .
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 5e+01 .

_:N80c91623373a353a57a815210000001f a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral .
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral ;
geo:hasMetricSpatialAccuracy 3e+01 .

_:N97499f6e93a23881f212924400000001 a geo:Geometry ;
geo:asWKT "<http://www.opengis.net/def/crs/EPSG/0/7844> POINT (-33.8 115.21)"^^geo:wktLiteral ;
Expand Down
14 changes: 8 additions & 6 deletions abis_mapping/templates/survey_occurrence_data_v2/mapping.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1784,6 +1784,13 @@ def add_sampling_field(
graph.add((uri, utils.namespaces.GEO.hasGeometry, geometry_node))
graph.add((geometry_node, a, utils.namespaces.GEO.Geometry))
graph.add((geometry_node, utils.namespaces.GEO.asWKT, geometry.to_transformed_crs_rdf_literal()))

spatial_accuracy = row["coordinateUncertaintyInMeters"]
accuracy = None
if spatial_accuracy is not None:
accuracy = rdflib.Literal(spatial_accuracy, datatype=rdflib.XSD.double)
graph.add((geometry_node, utils.namespaces.GEO.hasMetricSpatialAccuracy, accuracy))

graph.add((uri, rdflib.SOSA.hasResult, sample_field))

# Conditionally add survey
Expand All @@ -1800,6 +1807,7 @@ def add_sampling_field(
obj=geometry_node,
geom=geometry,
graph=graph,
spatial_accuracy=accuracy,
)

# Add site if one provided
Expand Down Expand Up @@ -1827,12 +1835,6 @@ def add_sampling_field(
# Add Location Description
graph.add((uri, utils.namespaces.TERN.locationDescription, rdflib.Literal(row["locality"])))

# Check for coordinateUncertaintyInMeters
if row["coordinateUncertaintyInMeters"]:
# Add Spatial Accuracy
accuracy = rdflib.Literal(row["coordinateUncertaintyInMeters"], datatype=rdflib.XSD.double)
graph.add((uri, utils.namespaces.GEO.hasMetricSpatialAccuracy, accuracy))

def add_provider_record_id_agent(
self,
uri: rdflib.URIRef,
Expand Down
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