Add migrator for differentiating metabolomics analyses

nmdc_schema/migrators/migrator_from_11_3_0_to_11_4_0.py

@@ -0,0 +1,35 @@
+from nmdc_schema.migrators.migrator_base import MigratorBase
+
+
+class Migrator(MigratorBase):
+    r"""Migrates a database between two schemas."""
+
+    _from_version = "11.3.0"
+    _to_version = "11.4.0"
+
+    def upgrade(self):
+        r"""Migrates the database from conforming to the original schema, to conforming to the new schema."""
+
+        self.adapter.process_each_document("workflow_execution_set", [self.set_metab_analysis_category])
+
+    def set_metab_analysis_category(self, workflow: dict) -> dict:
+        r"""
+        If the workflow execution records is of the type "nmdc:MetabolomicsAnalysis" and it has a `has_metabolite_identifications` field,
+        add field `metabolomics_analysis_category` and assign it the value "gc_ms_metabolomics". If the record does not 
+        have a `has_metabolite_identifications` field, it is assigned the value "lc_ms_lipidomics".
+
+        >>> m = Migrator()
+        >>> m.set_metab_analysis_category({'id': 123, 'type': 'nmdc:MetabolomicsAnalysis', 'has_metabolite_identifications': []})
+        {'id': 123, 'type': 'nmdc:MetabolomicsAnalysis', 'has_metabolite_identifications': [], 'metabolomics_analysis_category': 'gc_ms_metabolomics'}
+        >>> m.set_metab_analysis_category({'id': 123, 'type': 'nmdc:MetabolomicsAnalysis'})  # does not have has_metabolite_identifications field, therefore it's a lipid analysis
+        {'id': 123, 'type': 'nmdc:MetabolomicsAnalysis', 'metabolomics_analysis_category': 'lc_ms_lipidomics'}
+        >>> m.set_metab_analysis_category({'id': 123, 'type': 'nmdc:Metaproteomics')  # not a metabolomics analysis
+        {'id': 123, 'type': 'nmdc:Metaproteomics'}
+        """
+
+        if workflow["type"] == "nmdc:MetabolomicsAnalysis":
+            if "has_metabolite_identifications" in workflow:
+                workflow["metabolomics_analysis_category"] = "gc_ms_metabolomics"
+            else:
+                workflow["metabolomics_analysis_category"] = "lc_ms_lipidomics"
+        return workflow