Move the SESARTransformer to the latest version of the iSamples Core …

…JSON constants

isamples_sesar/metadata_constants.py

@@ -0,0 +1,46 @@
+"""
+String constants used in metadata transformation
+"""
+
+METADATA_SCHEMA = "$schema"
+METADATA_AT_ID = "@id"
+METADATA_LABEL = "label"
+METADATA_IDENTIFIER = "identifier"
+METADATA_SAMPLE_IDENTIFIER = "sample_identifier"
+METADATA_DESCRIPTION = "description"
+METADATA_HAS_CONTEXT_CATEGORY = "has_context_category"
+METADATA_HAS_CONTEXT_CATEGORY_CONFIDENCE = "has_context_category_confidence"
+METADATA_HAS_MATERIAL_CATEGORY = "has_material_category"
+METADATA_HAS_MATERIAL_CATEGORY_CONFIDENCE = "has_material_category_confidence"
+METADATA_HAS_SAMPLE_OBJECT_TYPE = "has_sample_object_type"
+METADATA_HAS_SAMPLE_OBJECT_TYPE_CONFIDENCE = "has_sample_object_type_confidence"
+METADATA_INFORMAL_CLASSIFICATION = "informal_classification"
+METADATA_KEYWORDS = "keywords"
+METADATA_KEYWORD = "keyword"
+METADATA_SCHEME_NAME = "scheme_name"
+METADATA_KEYWORD_URI = "keyword_uri"
+METADATA_PRODUCED_BY = "produced_by"
+METADATA_RESPONSIBILITY = "responsibility"
+METADATA_HAS_FEATURE_OF_INTEREST = "has_feature_of_interest"
+METADATA_RESULT_TIME = "result_time"
+METADATA_SAMPLING_SITE = "sampling_site"
+METADATA_SAMPLE_LOCATION = "sample_location"
+METADATA_LOCATION = "location"
+METADATA_ELEVATION = "elevation"
+METADATA_LATITUDE = "latitude"
+METADATA_LONGITUDE = "longitude"
+METADATA_PLACE_NAME = "place_name"
+METADATA_SUBSAMPLE = "subsample"
+METADATA_REGISTRANT = "registrant"
+METADATA_SAMPLING_PURPOSE = "sampling_purpose"
+METADATA_CURATION = "curation"
+METADATA_ACCESS_CONSTRAINTS = "access_constraints"
+METADATA_CURATION_LOCATION = "curation_location"
+METADATA_RELATED_RESOURCE = "related_resource"
+METADATA_RELATIONSHIP = "relationship"
+METADATA_TARGET = "target"
+METADATA_AUTHORIZED_BY = "authorized_by"
+METADATA_COMPLIES_WITH = "complies_with"
+METADATA_ROLE = "role"
+METADATA_NAME = "name"
+METADATA_LAST_MODIFIED_TIME = "last_modified_time"

isamples_sesar/sesar_transformer.py

@@ -2,6 +2,14 @@
 from typing import Optional
 import logging
 import h3
+
+from .metadata_constants import METADATA_LABEL, METADATA_SAMPLE_IDENTIFIER, METADATA_DESCRIPTION, \
+    METADATA_HAS_CONTEXT_CATEGORY, METADATA_HAS_MATERIAL_CATEGORY, METADATA_HAS_SAMPLE_OBJECT_TYPE, \
+    METADATA_INFORMAL_CLASSIFICATION, METADATA_KEYWORDS, METADATA_AT_ID, METADATA_PRODUCED_BY, \
+    METADATA_HAS_FEATURE_OF_INTEREST, METADATA_RESPONSIBILITY, METADATA_RESULT_TIME, METADATA_SAMPLING_SITE, \
+    METADATA_SAMPLE_LOCATION, METADATA_ELEVATION, METADATA_LATITUDE, METADATA_LONGITUDE, METADATA_PLACE_NAME, \
+    METADATA_REGISTRANT, METADATA_SAMPLING_PURPOSE, METADATA_CURATION, METADATA_ACCESS_CONSTRAINTS, \
+    METADATA_CURATION_LOCATION, METADATA_RELATED_RESOURCE, METADATA_AUTHORIZED_BY, METADATA_COMPLIES_WITH
 from .sample import Sample
 
 from .mapper import (
@@ -39,53 +47,49 @@ def transform(self) -> typing.Dict:
         specimen_categories = self.has_specimen_categories()
         transformed_record = {
             "$schema": "iSamplesSchemaCore1.0.json",
-            "@id": self.id_string(),
-            "label": self.sample_label(),
-            "sampleidentifier": self.sample_identifier_string(),
-            "description": self.sample_description(),
-            "hasContextCategory": context_categories,
+            METADATA_AT_ID: self.id_string(),
+            METADATA_LABEL: self.sample_label(),
+            METADATA_SAMPLE_IDENTIFIER: self.sample_identifier_string(),
+            METADATA_DESCRIPTION: self.sample_description(),
+            METADATA_HAS_CONTEXT_CATEGORY: context_categories,
             # "hasContextCategoryConfidence": self.has_context_category_confidences(context_categories),
-            "hasMaterialCategory": material_categories,
+            METADATA_HAS_MATERIAL_CATEGORY: material_categories,
             # "hasMaterialCategoryConfidence": self.has_material_category_confidences(material_categories),
-            "hasSpecimenCategory": specimen_categories,
+            METADATA_HAS_SAMPLE_OBJECT_TYPE: specimen_categories,
             # "hasSpecimenCategoryConfidence": self.has_specimen_category_confidences(specimen_categories),
-            "informalClassification": self.informal_classification(),
-            "keywords": self.keywords(),
-            "producedBy": {
-                "@id": self.produced_by_id_string(),
-                "label": self.produced_by_label(),
-                "description": self.produced_by_description(),
-                "hasFeatureOfInterest": self.produced_by_feature_of_interest(),
-                "responsibility": self.produced_by_responsibilities(),
-                "resultTime": self.produced_by_result_time(),
-                "samplingSite": {
-                    "description": self.sampling_site_description(),
-                    "label": self.sampling_site_label(),
-                    "location": {
-                        "elevation": self.sampling_site_elevation(),
-                        "latitude": self.sampling_site_latitude(),
-                        "longitude": self.sampling_site_longitude(),
+            METADATA_INFORMAL_CLASSIFICATION: self.informal_classification(),
+            METADATA_KEYWORDS: self.keywords(),
+            METADATA_PRODUCED_BY: {
+                METADATA_AT_ID: self.produced_by_id_string(),
+                METADATA_LABEL: self.produced_by_label(),
+                METADATA_DESCRIPTION: self.produced_by_description(),
+                METADATA_HAS_FEATURE_OF_INTEREST: self.produced_by_feature_of_interest(),
+                METADATA_RESPONSIBILITY: self.produced_by_responsibilities(),
+                METADATA_RESULT_TIME: self.produced_by_result_time(),
+                METADATA_SAMPLING_SITE: {
+                    METADATA_DESCRIPTION: self.sampling_site_description(),
+                    METADATA_LABEL: self.sampling_site_label(),
+                    METADATA_SAMPLE_LOCATION: {
+                        METADATA_ELEVATION: self.sampling_site_elevation(),
+                        METADATA_LATITUDE: self.sampling_site_latitude(),
+                        METADATA_LONGITUDE: self.sampling_site_longitude(),
                     },
-                    "placeName": self.sampling_site_place_names(),
+                    METADATA_PLACE_NAME: self.sampling_site_place_names(),
                 },
             },
-            "registrant": self.sample_registrant(),
-            "samplingPurpose": self.sample_sampling_purpose(),
-            "curation": {
-                "label": self.curation_label(),
-                "description": self.curation_description(),
-                "accessConstraints": self.curation_access_constraints(),
-                "curationLocation": self.curation_location(),
-                "responsibility": self.curation_responsibility(),
+            METADATA_REGISTRANT: self.sample_registrant(),
+            METADATA_SAMPLING_PURPOSE: self.sample_sampling_purpose(),
+            METADATA_CURATION: {
+                METADATA_LABEL: self.curation_label(),
+                METADATA_DESCRIPTION: self.curation_description(),
+                METADATA_ACCESS_CONSTRAINTS: self.curation_access_constraints(),
+                METADATA_CURATION_LOCATION: self.curation_location(),
+                METADATA_RESPONSIBILITY: self.curation_responsibility(),
             },
-            "relatedResource": self.related_resources(),
-            "authorizedBy": self.authorized_by(),
-            "compliesWith": self.complies_with(),
+            METADATA_RELATED_RESOURCE: self.related_resources(),
+            METADATA_AUTHORIZED_BY: self.authorized_by(),
+            METADATA_COMPLIES_WITH: self.complies_with(),
         }
-        for index in range(0, 15):
-            h3_at_resolution = self.h3_function()(self.sample.latitude, self.sample.longitude, index)
-            field_name = f"producedBy_samplingSite_location_h3_{index}"
-            transformed_record[field_name] = h3_at_resolution
         return transformed_record
 
     def has_context_categories(self) -> typing.List[str]: