Sample Json Parser sceleton class.

Author: Milo Hyben

metamist/parser/sample_json_parser.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+# pylint: disable=too-many-instance-attributes,too-many-locals,unused-argument,wrong-import-order,unused-argument
+from typing import List
+import logging
+
+from metamist.parser.generic_metadata_parser import (
+    GenericMetadataParser
+)
+from metamist.parser.generic_parser import SingleRow
+
+logger = logging.getLogger(__file__)
+logger.addHandler(logging.StreamHandler())
+logger.setLevel(logging.INFO)
+
+__DOC = """
+Sample JSON parser - TODO add more details
+
+JSON data example:
+{"identifier": "AB0002", "name": "j smith", "age": 50, "dob": "5/05/1950", "measurement": "98.7", "observation": "B++", "receipt_date": "1/02/2023"}
+
+"""
+
+
+class SampleJsonColumns:
+    """Column keys for JSON Sample Data"""
+
+    IDENTIFIER = 'identifier'
+    NAME = 'name'
+    AGE = 'age'
+    DOB = 'dob'
+    MEASUREMENT = 'measurement'
+    OBSERVATION = 'observation'
+    RECEIPT_DATE = 'receipt_date'
+    
+    @staticmethod
+    def participant_meta_map():
+        """Participant meta map"""
+        return {}
+    
+    @staticmethod
+    def sequence_meta_map():
+        """Columns that will be put into sequence.meta"""
+        return {}
+
+    @staticmethod
+    def sample_meta_map():
+        """Columns that will be put into sample.meta"""
+        return {}
+
+
+class SampleJsonParser(GenericMetadataParser):
+    """Parser for Sample JSON Records"""
+
+    def __init__(
+        self,
+        project: str
+    ):
+        super().__init__(
+            project=project,
+            participant_meta_map=SampleJsonColumns.participant_meta_map(),
+            sample_meta_map=SampleJsonColumns.sample_meta_map(),
+            assay_meta_map=SampleJsonColumns.sequence_meta_map()
+        )
+
+