Merge pull request #354 from gaiaresources/BDRSPS-1086

BDRSPS-1086 Don't create the record number datatype when there is no `recordNumber` field

abis_mapping/templates/incidental_occurrence_data_v3/examples/margaret_river_flora/margaret_river_flora.csv

@@ -1,7 +1,7 @@
 providerRecordID,providerRecordIDSource,locality,decimalLatitude,decimalLongitude,geodeticDatum,coordinateUncertaintyInMeters,dataGeneralizations,eventDateStart,eventDateEnd,samplingProtocol,basisOfRecord,recordedBy,recordNumber,occurrenceStatus,habitat,establishmentMeans,organismRemarks,individualCount,organismQuantity,organismQuantityType,lifeStage,sex,reproductiveCondition,ownerRecordID,ownerRecordIDSource,collectionCode,catalogNumber,catalogNumberSource,otherCatalogNumbers,otherCatalogNumbersSource,preparations,preparedDate,associatedSequences,sequencingMethod,verbatimIdentification,dateIdentified,identifiedBy,identificationMethod,scientificName,identificationQualifier,identificationRemarks,acceptedNameUsage,kingdom,taxonRank,threatStatus,conservationAuthority,threatStatusCheckProtocol,threatStatusDateDetermined,threatStatusDeterminedBy,sensitivityCategory,sensitivityAuthority
 1,WAM,Cowaramup Bay Road,-33.8,115.21,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Calothamnus lateralis var. crassus,,Stream Environment and Water Pty Ltd,,Calothamnus lateralis var. crassus,,,,Plantae,,,,,,,,
-2,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,
-3,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,
+2,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,,PE:12:8831,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,
+3,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,Test Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,
 4,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,
 5,WAM,Cowaramup Bay Road,-33.86,114.99,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Banksia sessilis var. cordata,,Stream Environment and Water Pty Ltd,,Banksia sessilis var. cordata,,,,Plantae,,,,,,,,
 6,WAM,Cowaramup Bay Road,-33.86,114.99,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Banksia sessilis var. cordata,,Stream Environment and Water Pty Ltd,,Banksia sessilis var. cordata,,,,Plantae,,,,,,,,

abis_mapping/templates/incidental_occurrence_data_v3/examples/margaret_river_flora/margaret_river_flora.ttl

@@ -1323,6 +1323,9 @@
 <https://linked.data.gov.au/dataset/bdr/orgs/BHP> a prov:Agent ;
     schema:name "BHP" .
 
+<https://linked.data.gov.au/dataset/bdr/orgs/Test-Pty-Ltd> a prov:Agent ;
+    schema:name "Test Pty Ltd" .
+
 <https://linked.data.gov.au/dataset/bdr/orgs/WA-BIO> a prov:Agent ;
     schema:name "WA-BIO" .
 
@@ -1530,8 +1533,8 @@
 
 <http://createme.org/occurrence/2> a dwc:Occurrence,
         tern:FeatureOfInterest ;
-    prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
+    schema:identifier "PE:12:8831" ;
     schema:isPartOf <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
     schema:spatial _:N489292b7f1191795326ddd2200000003 ;
     schema:temporal [ a time:TemporalEntity ;
@@ -1542,7 +1545,7 @@
 
 <http://createme.org/occurrence/3> a dwc:Occurrence,
         tern:FeatureOfInterest ;
-    prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
+    prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Test-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
     schema:isPartOf <http://createme.org/dataset/Example-Incidental-Occurrence-Dataset> ;
     schema:spatial _:N489292b7f1191795326ddd2200000006 ;

abis_mapping/templates/incidental_occurrence_data_v3/mapping.py

@@ -512,7 +512,7 @@ def apply_mapping_row(
         self.add_record_number_datatype(
             uri=record_number_datatype,
             provider=provider_recorded_by,
-            value=recorded_by,
+            row=row,
             graph=graph,
         )
 
@@ -1851,7 +1851,7 @@ def add_record_number_datatype(
         self,
         uri: rdflib.URIRef | None,
         provider: rdflib.URIRef | None,
-        value: str | None,
+        row: frictionless.Row,
         graph: rdflib.Graph,
     ) -> None:
         """Adds record number datatype to the graph.
@@ -1861,19 +1861,23 @@ def add_record_number_datatype(
                 or None if uri wasn't created.
             provider (rdflib.URIRef | None): The corresponding
                 provider uri.
-            value (str | None): Raw value provided in row.
+            row (frictionless.Row): Row from the template.
             graph (rdflib.Graph): Graph to be modified.
         """
         # Check subject provided
         if uri is None:
             return
 
+        # if no recordNumber, don't create this datatype because it would be unused.
+        if not row["recordNumber"]:
+            return
+
         # Add type
         graph.add((uri, a, rdflib.RDFS.Datatype))
 
         # Add label
-        if value is not None:
-            graph.add((uri, rdflib.SKOS.prefLabel, rdflib.Literal(f"{value} recordNumber")))
+        if recorded_by := row["recordedBy"]:
+            graph.add((uri, rdflib.SKOS.prefLabel, rdflib.Literal(f"{recorded_by} recordNumber")))
 
         # Add definition
         graph.add(

abis_mapping/templates/survey_occurrence_data_v2/examples/margaret_river_flora/margaret_river_flora.csv

@@ -1,7 +1,7 @@
 providerRecordID,providerRecordIDSource,locality,decimalLatitude,decimalLongitude,geodeticDatum,coordinateUncertaintyInMeters,dataGeneralizations,eventDateStart,eventDateEnd,samplingProtocol,basisOfRecord,recordedBy,recordNumber,occurrenceStatus,habitat,establishmentMeans,organismRemarks,individualCount,organismQuantity,organismQuantityType,lifeStage,sex,reproductiveCondition,ownerRecordID,ownerRecordIDSource,collectionCode,catalogNumber,catalogNumberSource,otherCatalogNumbers,otherCatalogNumbersSource,preparations,preparedDate,associatedSequences,sequencingMethod,verbatimIdentification,dateIdentified,identifiedBy,identificationMethod,scientificName,identificationQualifier,identificationRemarks,acceptedNameUsage,kingdom,taxonRank,threatStatus,conservationAuthority,threatStatusCheckProtocol,threatStatusDateDetermined,threatStatusDeterminedBy,sensitivityCategory,sensitivityAuthority,surveyID,siteID,siteVisitID
 1,WAM,Cowaramup Bay Road,-33.8,115.21,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Calothamnus lateralis var. crassus,,Stream Environment and Water Pty Ltd,,Calothamnus lateralis var. crassus,,,,Plantae,,,,,,,,,,,
-2,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,,,,
-3,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,,,,
+2,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,,PE:12:8831,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,,,,
+3,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,Test Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,,,,
 4,WAM,Cowaramup Bay Road,-33.86,115.01,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Boronia anceps,,Stream Environment and Water Pty Ltd,,Boronia anceps,,,,Plantae,,,,,,,,,,,
 5,WAM,Cowaramup Bay Road,-33.86,114.99,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Banksia sessilis var. cordata,,Stream Environment and Water Pty Ltd,,Banksia sessilis var. cordata,,,,Plantae,,,,,,,,,,,
 6,WAM,Cowaramup Bay Road,-33.86,114.99,WGS84,,,26/09/2019,,,,Stream Environment and Water Pty Ltd,,,,,,,,,,,,,,,,,,,,,,,Banksia sessilis var. cordata,,Stream Environment and Water Pty Ltd,,Banksia sessilis var. cordata,,,,Plantae,,,,,,,,,,,

abis_mapping/templates/survey_occurrence_data_v2/examples/margaret_river_flora/margaret_river_flora.ttl

@@ -1308,6 +1308,9 @@
 <https://linked.data.gov.au/dataset/bdr/orgs/BHP> a prov:Agent ;
     schema:name "BHP" .
 
+<https://linked.data.gov.au/dataset/bdr/orgs/Test-Pty-Ltd> a prov:Agent ;
+    schema:name "Test Pty Ltd" .
+
 <https://linked.data.gov.au/dataset/bdr/orgs/WA-BIO> a prov:Agent ;
     schema:name "WA-BIO" .
 
@@ -1527,8 +1530,8 @@
 
 <http://createme.org/occurrence/2> a dwc:Occurrence,
         tern:FeatureOfInterest ;
-    prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
+    schema:identifier "PE:12:8831" ;
     schema:isPartOf <http://createme.org/Survey/1>,
         <http://createme.org/dataset/Example-Systematic-Survey-Occurrence-Dataset> ;
     schema:spatial _:N1dddcc66c58fa593aae7f72f00000003 ;
@@ -1540,7 +1543,7 @@
 
 <http://createme.org/occurrence/3> a dwc:Occurrence,
         tern:FeatureOfInterest ;
-    prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Stream-Environment-and-Water-Pty-Ltd> ;
+    prov:wasAssociatedWith <https://linked.data.gov.au/dataset/bdr/orgs/Test-Pty-Ltd> ;
     sosa:usedProcedure <https://linked.data.gov.au/def/nrm/a8db263e-7a39-5b85-a5d2-8e1af7ce1e39> ;
     schema:isPartOf <http://createme.org/Survey/1>,
         <http://createme.org/dataset/Example-Systematic-Survey-Occurrence-Dataset> ;

abis_mapping/templates/survey_occurrence_data_v2/mapping.py

@@ -672,7 +672,7 @@ def apply_mapping_row(
         self.add_record_number_datatype(
             uri=record_number_datatype,
             provider=provider_recorded_by,
-            value=recorded_by,
+            row=row,
             graph=graph,
         )
 
@@ -2189,7 +2189,7 @@ def add_record_number_datatype(
         self,
         uri: rdflib.URIRef | None,
         provider: rdflib.URIRef | None,
-        value: str | None,
+        row: frictionless.Row,
         graph: rdflib.Graph,
     ) -> None:
         """Adds record number datatype to the graph.
@@ -2198,19 +2198,23 @@ def add_record_number_datatype(
                 or None if uri wasn't created.
             provider (rdflib.URIRef | None): The corresponding
                 provider uri.
-            value (str | None): Raw value provided in row.
+            row (frictionless.Row): Row from the template.
             graph (rdflib.Graph): Graph to be modified.
         """
         # Check subject provided
         if uri is None:
             return
 
+        # if no recordNumber, don't create this datatype because it would be unused.
+        if not row["recordNumber"]:
+            return
+
         # Add type
         graph.add((uri, a, rdflib.RDFS.Datatype))
 
         # Add label
-        if value is not None:
-            graph.add((uri, rdflib.SKOS.prefLabel, rdflib.Literal(f"{value} recordNumber")))
+        if recorded_by := row["recordedBy"]:
+            graph.add((uri, rdflib.SKOS.prefLabel, rdflib.Literal(f"{recorded_by} recordNumber")))
 
         # Add definition
         graph.add(