Merge pull request #198 from gaiaresources/BDRSPS-779

BDRSPS-779 Added basic files for the site visit template.

abis_mapping/base/mapper.py

@@ -3,6 +3,7 @@
 
 # Standard
 import abc
+import csv
 import functools
 import inspect
 import json
@@ -126,6 +127,25 @@ def add_geometry_supplied_as(
         graph.add((supplied_as, utils.namespaces.GEO.asWKT, geom.to_rdf_literal()))
         graph.add((top_node, utils.namespaces.GEO.hasGeometry, supplied_as))
 
+    @classmethod
+    def generate_blank_template(cls) -> None:
+        """Generates a blank csv for the template.
+
+        It is based on the schema field names and writes it to a file within
+        the template mapper's root dir. Note: full schema validation is not applied,
+        and metadata validation is.
+        """
+        # Retrieve Schema Filepath
+        directory = pathlib.Path(inspect.getfile(cls)).parent
+        schema_file = directory / "schema.json"
+
+        # Get raw schema
+        fields: list[dict] = json.loads(schema_file.read_text())["fields"]
+        out_path = directory / f"{cls.metadata()['name']}.{cls.metadata()['file_type'].lower()}"
+        with out_path.open('w') as f:
+            csv_writer = csv.DictWriter(f, [field["name"] for field in fields])
+            csv_writer.writeheader()
+
     @classmethod
     def add_extra_fields_json(
         cls,

abis_mapping/templates/survey_site_data_v2/mapping.py

@@ -1,4 +1,4 @@
-"""Provides ABIS Mapper for `survey_site_data.csv` Template v2"""
+"""Provides ABIS Mapper for `survey_site_data-v2.0.0.csv` template."""
 
 # Standard
 import dataclasses

abis_mapping/templates/survey_site_visit_data_v2/README.md

@@ -0,0 +1,5 @@
+# Template Description
+A template to translate some Darwin Core fields 
+
+# Template Instructions
+See `instructions.pdf` for more details

abis_mapping/templates/survey_site_visit_data_v2/mapping.py

@@ -0,0 +1,85 @@
+"""Provides ABIS Mapper for `survey_site_visit_data-v2.0.0` template."""
+
+# Third-party
+import frictionless
+import rdflib
+
+# Local
+from abis_mapping import base
+
+# Typing
+from typing import Any, Iterator
+
+
+class SurveySiteVisitMapper(base.mapper.ABISMapper):
+    """ABIS mapper for the v2 survey site data csv template."""
+
+    # Default Dataset Metadata
+    DATASET_DEFAULT_NAME = "Example Systematic Survey Site Visit Dataset"
+    DATASET_DEFAULT_DESCRIPTION = "Example Systematic Survey Site Visit Dataset by Gaia Resources"
+
+    def apply_validation(
+        self,
+        data: base.types.ReadableType,
+        **kwargs: Any,
+    ) -> frictionless.Report:
+        """Applies Frictionless Validation for the csv Template
+
+        Args:
+            data (base.types.ReadableType): Raw data to be validated.
+            **kwargs (Any): Additional keyword arguments.
+
+        Keyword Args:
+            site_visit_id_map (dict[str, bool]): Site visit ids present in the occurrence template.
+
+        Returns:
+            frictionless.Report: Validation report for the specified data.
+        """
+        # TODO: Implement
+        raise NotImplementedError
+
+        # Extract keyword arguments
+        # TODO: Uncomment
+        # site_visit_id_map: dict[str, bool] = kwargs.get("site_visit_id_map", {})
+
+        # Construct schema
+        schema = self.extra_fields_schema(data=data, full_schema=True)
+
+        # Construct resource
+        resource = frictionless.Resource(
+            source=data,
+            format="csv",
+            schema=schema,
+            encoding="utf-8",
+        )
+
+        # Validate
+        report = resource.validate()
+
+        # Return validation report
+        return report
+
+    def apply_mapping(
+        self,
+        data: base.types.ReadableType,
+        dataset_iri: rdflib.URIRef | None = None,
+        base_iri: rdflib.Namespace | None = None,
+        **kwargs: Any,
+    ) -> Iterator[rdflib.Graph]:
+        """Applies Mapping from Raw Data to ABIS conformant RDF.
+
+        Args:
+            data (ReadableType): Readable raw data.
+            dataset_iri (Optional[rdflib.URIRef]): Optional dataset IRI.
+            base_iri (Optional[rdflib.Namespace]): Optional mapping base IRI.
+            **kwargs (Any): Additional keyword arguments.
+
+        Keyword Args:
+            chunk_size (Optional[int]): How many rows of the original data to
+                ingest before yielding a graph. `None` will ingest all rows.
+
+        Yields:
+            rdflib.Graph: ABIS Conformant RDF Sub-Graph from Raw Data Chunk.
+        """
+        # TODO: Implement
+        raise NotImplementedError

abis_mapping/templates/survey_site_visit_data_v2/metadata.json

@@ -0,0 +1,13 @@
+{
+	"name": "survey_site_visit_data",
+	"label": "Systematic Survey Site Visit Data Template",
+	"version": "2.0.0",
+	"description": "A template for systematic survey site visit data",
+	"biodiversity_type": "Systematic Survey Site Visit Data",
+	"spatial_type": "Point, line, polygon",
+	"file_type": "CSV",
+	"sampling_type": "systematic survey",
+	"template_url": "https://raw.githubusercontent.com/gaiaresources/abis-mapping/main/abis_mapping/templates/survey_site_visit_data_v2/survey_site_visit_data.csv",
+	"schema_url": "https://raw.githubusercontent.com/gaiaresources/abis-mapping/main/abis_mapping/templates/survey_site_visit_data_v2/schema.json",
+	"instructions_url": "https://raw.githubusercontent.com/gaiaresources/abis-mapping/main/abis_mapping/templates/survey_site_visit_data_v2/instructions.pdf"
+}

abis_mapping/templates/survey_site_visit_data_v2/schema.json

@@ -0,0 +1,167 @@
+{
+	"fields": [
+		{
+			"name": "surveyID",
+			"title": "SurveyID",
+			"description": "The identifier of the Survey that the Site is related to in this dataset.",
+			"example": "AR220-01",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"name": "siteID",
+			"title": "Site ID",
+			"description": "A unique within dataset string identifier for the site. Valid values include strings that are used specifically for this survey or URIs from BDR Sites that have been established in previous surveys.",
+			"example": "P1",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": true,
+				"unique": true
+			}
+		},
+		{
+			"name": "siteIDSource",
+			"title": "Site ID Source",
+			"description": "The organisation that assigned the SiteID to this Site",
+			"example": "TERN",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"name": "siteVisitID",
+			"title": "Site Visit ID",
+			"description": "The unique key assigned to a visit. A visit is a time distinct assessment conducted within a survey at a designated site.",
+			"example": "CPXEI0000001",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": true,
+				"unique": true
+			}
+		},
+		{
+			"name": "siteVisitStart",
+			"title": "Site Visit Start",
+			"description": "The temporal start of when the Site was being used to collect data for the survey. Expected values include date, dateTime, dateTimeStamp.",
+			"example": "2016-02-28",
+			"type": "timestamp",
+			"format": "default",
+			"constraints": {
+				"required": true
+			}
+		},
+		{
+			"name": "siteVisitEnd",
+			"title": "Site Visit End",
+			"description": "The temporal end of when the Site was being used to collect data for the survey. Expected values include date, dateTime, dateTimeStamp.",
+			"example": "2016-02-28",
+			"type": "timestamp",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"name": "visitOrgs",
+			"title": "Visit Orgs",
+			"description": "The names of the organisations responsible for recording the original Occurrence.",
+			"example": "NSW Dept of Planning, Industry and Environment.",
+			"type": "list",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"name": "visitObservers",
+			"title": "Visit Observers",
+			"description": "A list (concatenated and separated using |) of names of people, groups, or organisations responsible for recording the original Occurrence.",
+			"example": "Oliver P. Pearson | Anita K. Pearson",
+			"type": "list",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"name": "condition",
+			"title": "Condition",
+			"description": "The state of a patch of vegetation at the time of sampling relative to some specified standard or benchmark (where available).",
+			"example": "Burnt",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"name": "targetTaxonomicScope",
+			"title": "Target Taxonomic Scope",
+			"description": "The taxonomic group targeted for sampling during the Site Visit",
+			"example": "Coleoptera",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"_comment": "can we do a flexible vocabulary while I do the recon to establish the concepts?",
+			"name": "protocolName",
+			"title": "Protocol Name",
+			"description": "Categorical descriptive name for the method used during the Site Visit.",
+			"example": "harpTrapping",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": false
+			},
+			"vocabularies": [
+				"VISIT_PROTOCOL_NAME"
+			]
+		},
+		{
+			"name": "protocolDescription",
+			"title": "Protocol Description",
+			"description": "A detailed description of the method used during the Site Visit. The description may include deviations from a protocol referred to in eco:protocolReferences. Recommended good practice is to provide information about instruments used, calibration, etc.",
+			"example": "Three conventional harp traps (3.2m ht x 2.2m w) were established in flight path zones for a period of 4 hrs at dawn and dusk for a total of 10 trap nights. Traps were visited on an hourly basis during each deployment period and the trap catch recorded for species, size, weight, sex, age and maternal status.",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"name": "samplingEffortValue",
+			"title": "Sample Effort",
+			"description": "Similar to eco:samplingEffortValue. The total sampling effort value. A samplingEffortValue must have a corresponding samplingEffortUnit",
+			"example": "20 x 12",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": false
+			}
+		},
+		{
+			"name": "samplingEffortUnit",
+			"title": "Sampling Effort Units",
+			"description": "Similar to eco:samplingEffortUnit. The units associated with samplingEffortValue.",
+			"example": "trapDays",
+			"type": "string",
+			"format": "default",
+			"constraints": {
+				"required": false
+			},
+			"vocabularies": [
+				"SAMPLING_EFFORT_UNIT"
+			]
+		}
+	]
+}

abis_mapping/templates/survey_site_visit_data_v2/survey_site_visit_data.csv

@@ -0,0 +1 @@
+surveyID,siteID,siteIDSource,siteVisitID,siteVisitStart,siteVisitEnd,visitOrgs,visitObservers,condition,targetTaxonomicScope,protocolName,protocolDescription,samplingEffortValue,samplingEffortUnit