BDRSPS-883 Added specific implementation for the occurrence field tablers to include vocab links to the threatStatus table

abis_mapping/templates/incidental_occurrence_data_v2/templates/instructions.md

@@ -104,7 +104,7 @@ must come from one of five options in this table.</font></ins>
 
 {{tables.vocabularies}}
 
-<a name="threatStatus-vocabularies"></a>
+<a name="threatStatus-vocabularies"></a><a name="conservationJurisdiction-vocabularies"></a>
 <ins>Table 2b: Suggested values for conditionally mandatory values for the threatStatus and
 conservationJurisdiction in the template. State and Territory conservationJurisdictions spelt out
 in words are also valid. For some threatStatus terms, alternative labels are provided that are also

abis_mapping/templates/incidental_occurrence_data_v3/templates/instructions.md

@@ -99,7 +99,7 @@ must come from one of five options in this table.</font></ins>
 
 {{tables.vocabularies}}
 
-<a name="threatStatus-vocabularies"></a>
+<a name="threatStatus-vocabularies"></a><a name="conservationAuthority-vocabularies"></a>
 <ins>Table 2b: Suggested values for conditionally mandatory values for the threatStatus and
 conservationAuthority in the template. State and Territory Conservation Authorities spelt out
 in words are also valid. For some threatStatus terms, alternative labels are provided that are also

abis_mapping/templates/survey_occurrence_data/templates/instructions.md

@@ -94,7 +94,7 @@ labels with similar semantics are provided. Note: <font color="red">`geodeticDat
 
 {{tables.vocabularies}}
 
-<a name="threatStatus-vocabularies"></a>
+<a name="threatStatus-vocabularies"></a><a name="conservationJurisdiction-vocabularies"></a>
 <ins>Table 2b: Suggested values for conditionally mandatory values for the `threatStatus` and
 `conservationJurisdiction` fields in the template. State and Territory `conservationJurisdictions` 
 spelt out as words are also valid. For some `threatStatus` terms, alternative labels are provided

abis_mapping/templates/survey_occurrence_data_v2/templates/instructions.md

@@ -106,7 +106,7 @@ labels with similar semantics are provided. Note: <font color="red">`geodeticDat
 
 {{tables.vocabularies}}
 
-<a name="threatStatus-vocabularies"></a>
+<a name="threatStatus-vocabularies"></a><a name="conservationAuthority-vocabularies"></a>
 <ins>Table 2b: Suggested values for conditionally mandatory values for the `threatStatus` and
 `conservationAuthority` fields in the template. State and Territory `conservationAuthority` 
 spelt out as words are also valid. For some `threatStatus` terms, alternative labels are provided

docs/contexts/incidental_occurrence_data_v2.py

@@ -16,7 +16,7 @@
 # Create context
 _ctx = {
     "tables": {
-        "fields": tables.fields.FieldTabler(template_id=mapper_id, format="markdown").generate_table(),
+        "fields": tables.fields.OccurrenceFieldTabler(template_id=mapper_id, format="markdown").generate_table(),
         "vocabularies": tables.vocabs.VocabTabler(template_id=mapper_id, format="markdown").generate_table(),
         "threat_status": tables.threat_status.ThreatStatusTabler(
             template_id=mapper_id, format="markdown"

docs/contexts/incidental_occurrence_data_v3.py

@@ -22,7 +22,7 @@ def _ctx() -> dict[str, Any]:
     # Return
     return {
         "tables": {
-            "fields": tables.fields.FieldTabler(template_id=mapper_id, format="markdown").generate_table(),
+            "fields": tables.fields.OccurrenceFieldTabler(template_id=mapper_id, format="markdown").generate_table(),
             "vocabularies": tables.vocabs.VocabTabler(template_id=mapper_id, format="markdown").generate_table(),
             "threat_status": tables.threat_status.ThreatStatusTabler(
                 template_id=mapper_id, format="markdown"

docs/contexts/survey_occurrence_data.py

@@ -16,7 +16,7 @@
 # Create context
 _ctx = {
     "tables": {
-        "fields": tables.fields.FieldTabler(template_id=mapper_id, format="markdown").generate_table(),
+        "fields": tables.fields.OccurrenceFieldTabler(template_id=mapper_id, format="markdown").generate_table(),
         "vocabularies": tables.vocabs.VocabTabler(
             template_id=mapper_id,
             format="markdown",

docs/contexts/survey_occurrence_data_v2.py

@@ -22,7 +22,7 @@ def _ctx() -> dict[str, Any]:
     # Return
     return {
         "tables": {
-            "fields": tables.fields.FieldTabler(template_id=mapper_id, format="markdown").generate_table(),
+            "fields": tables.fields.OccurrenceFieldTabler(template_id=mapper_id, format="markdown").generate_table(),
             "vocabularies": tables.vocabs.VocabTabler(template_id=mapper_id, format="markdown").generate_table(),
             "threat_status": tables.threat_status.ThreatStatusTabler(
                 template_id=mapper_id, format="markdown"

docs/tables/fields.py

@@ -42,6 +42,17 @@ def header(self) -> list[str]:
         raw_hdr = (hdr.serialization_alias or hdr.title for hdr in FieldTableRow.model_fields.values())
         return [hdr for hdr in raw_hdr if hdr is not None]
 
+    @property
+    def fields(self) -> list[types.schema.Field]:
+        """Getter for the fields.
+
+        Returns:
+            list[types.schema.Field]: List of all fields from schema.
+        """
+        # Get fields from schema and return
+        dict_fields = self.mapper.schema()["fields"]
+        return [types.schema.Field.model_validate(f) for f in dict_fields]
+
     def generate_table(
         self,
         dest: IO | None = None,
@@ -60,12 +71,8 @@ def generate_table(
         # Write header
         self.writer.writeheader()
 
-        # Localize fields
-        dict_fields = self.mapper.schema()["fields"]
-        fields: list[types.schema.Field] = [types.schema.Field.model_validate(f) for f in dict_fields]
-
         # Iterate through fields and add to csv
-        for field in fields:
+        for field in self.fields:
             # Perform basic mapping initially
             field_table_row = self.generate_row(field)
 
@@ -210,6 +217,47 @@ def mutual_inclusivity(field_name: str, checklist: frictionless.Checklist) -> se
         return fields
 
 
+class OccurrenceField(types.schema.Field):
+    """Specific implementation of the field model.
+
+    To be used only in the creation of survey and incidental occurrence field tables.
+    """
+
+    @property
+    def publishable_vocabularies(self) -> list[str]:
+        """Returns a list of only those vocabularies that are publishable.
+
+        Returns:
+            list[str]: The publishable vocabularies.
+        """
+        # Filter and return
+        vocabs = []
+        for v_id in self.vocabularies:
+            v = self.get_vocab(v_id)
+            # Modified from normal case threatStatus and conservationAuthority fields to make them
+            # publishable so links are created for their corresponding vocab which is
+            # currently its own table in the instructions.
+            if v.publish or v.vocab_id in ["THREAT_STATUS", "CONSERVATION_AUTHORITY"]:
+                vocabs.append(v_id)
+        return vocabs
+
+
+class OccurrenceFieldTabler(FieldTabler):
+    """Specific implementation of the field tabler for survey and incidental occurrence templates."""
+
+    @property
+    def fields(self) -> list[types.schema.Field]:
+        """Getter for the fields.
+
+        Returns:
+            list[OccurrenceField]: List of all fields from schema. Note: this specifically
+                returns OccurrenceField object list
+        """
+        # Get fields from schema and return
+        dict_fields = self.mapper.schema()["fields"]
+        return [OccurrenceField.model_validate(f) for f in dict_fields]
+
+
 if __name__ == "__main__":
     """Main entry point."""
     # Create argument parser