add migrator for moving relevant_protocols to protocol_link PR21

nmdc_schema/migrators/migrator_from_X_to_PR21.py

@@ -0,0 +1,48 @@
+from nmdc_schema.migrators.migrator_base import MigratorBase
+from nmdc_schema.migrators.helpers import load_yaml_asset
+
+class Migrator(MigratorBase):
+    """Migrates data from schema X to PR21"""
+
+    _from_version = "X"
+    _to_version = "PR21"
+
+    def __init__(self, *args, **kwargs) -> None:
+        """Invokes parent constructor and populates collection-to-transformations map."""
+
+        super().__init__(*args, **kwargs)
+
+        # Populate the "collection-to-transformers" map for this specific migration.
+        self._agenda = dict(
+            study_set=[self.move_relevant_protocols_to_protocol_link],
+        )
+
+    def move_relevant_protocols_to_protocol_link(self, study: dict):
+        r"""
+        Moves any urls that exist in the relevant_protocols slot to a dictionary format (e.g. Protocol class is the range) 
+        in the protocol_link slot. It then removes the relevant_protocols slot from the study.
+
+        >>> m = Migrator()
+        >>> m.move_relevant_protocols_to_protocol_link({'id': 123, 'relevant_protocols': ['www.ex1.org', 'www.ex2.gov']})
+        {'id': 123, 'protocol_link': [{'url': 'www.ex1.org', 'type': 'nmdc:Protocol'}, {'url': 'www.ex2.gov', 'type': 'nmdc:Protocol'}]}
+        >>> m.move_relevant_protocols_to_protocol_link({'id': 123, 'relevant_protocols': ['www.ex3.org']})
+        {'id': 123, 'protocol_link': [{'url': 'www.ex3.org', 'type': 'nmdc:Protocol'}]}
+        """
+
+        if "relevant_protocols" in study:
+            id = study["id"]
+            study["protocol_link"] = []
+            for protocol in study["relevant_protocols"]:
+                new_protocol_struct = {
+                    "url": protocol,
+                    "type": "nmdc:Protocol"
+                }
+                study["protocol_link"].append(new_protocol_struct)
+            self.logger.info(f"Moving {protocol} for study{id} from relevant_protocols slot to protocol_link")
+
+            study.pop("relevant_protocols")  
+
+
+        return study
+
+

project.Makefile

@@ -636,5 +636,4 @@ local/nmdc-sty-11-aygzgv51-tdb: local/nmdc-schema-v8.0.0.owl.ttl local/nmdc-sty-
 .PHONY: filtered-status
 filtered-status:
 	git status | grep -v 'project/' | grep -v 'nmdc_schema/.*yaml' | grep -v 'nmdc_schema/.*json' | \
-		grep -v 'nmdc.py' | grep -v 'nmdc_schema_accepting_legacy_ids.py'
-
+		grep -v 'nmdc.py' | grep -v 'nmdc_schema_accepting_legacy_ids.py'