Other approach

preprocessing/nextclade/src/loculus_preprocessing/datatypes.py

@@ -1,4 +1,4 @@
-# ruff: noqa: N815
+from collections import defaultdict
 from dataclasses import dataclass, field
 from enum import StrEnum, unique
 from typing import Any
@@ -79,7 +79,7 @@ class UnprocessedAfterNextclade:
     # Derived metadata produced by Nextclade
     nextcladeMetadata: dict[SegmentName, Any] | None
     unalignedNucleotideSequences: dict[SegmentName, NucleotideSequence | None]
-    alignedNucleotideSequences: dict[SegmentName, NucleotideSequence | None]
+    alignedNucleotideSequences: dict[GeneName, NucleotideSequence | None]
     nucleotideInsertions: dict[SegmentName, list[NucleotideInsertion]]
     alignedAminoAcidSequences: dict[GeneName, AminoAcidSequence | None]
     aminoAcidInsertions: dict[GeneName, list[AminoAcidInsertion]]
@@ -115,3 +115,67 @@ class ProcessingResult:
     datum: ProcessedMetadataValue
     warnings: list[ProcessingAnnotation] = field(default_factory=list)
     errors: list[ProcessingAnnotation] = field(default_factory=list)
+
+
+@dataclass
+class UnprocessedEntryFactory:
+    _counter: int = 0
+
+    @staticmethod
+    def create_unprocessed_entry(
+        metadata_dict: dict[str, str],
+    ) -> UnprocessedEntry:
+        unique_id = str(UnprocessedEntryFactory._counter)
+        UnprocessedEntryFactory._counter += 1
+        return UnprocessedEntry(
+            accessionVersion="LOC_" + unique_id + ".1",
+            data=UnprocessedData(
+                submitter="test_submitter",
+                metadata=metadata_dict,
+                unalignedNucleotideSequences={"main": ""},
+            ),
+        )
+
+
+@dataclass
+class ProcessedEntryFactory:
+    _counter: int = 0
+
+    @staticmethod
+    def create_processed_entry(
+        metadata_dict: dict[str, str],
+        metadata_errors: list[tuple[str, str]] | None = None,
+        metadata_warnings: list[tuple[str, str]] | None = None,
+    ) -> ProcessedEntry:
+        if metadata_errors is None:
+            metadata_errors = []
+        if metadata_warnings is None:
+            metadata_warnings = []
+        unique_id = str(ProcessedEntryFactory._counter)
+        ProcessedEntryFactory._counter += 1
+        return ProcessedEntry(
+            accession="LOC_" + unique_id,
+            version=1,
+            data=ProcessedData(
+                metadata=metadata_dict,
+                unalignedNucleotideSequences={"main": ""},
+                alignedNucleotideSequences={"main": None},
+                nucleotideInsertions={"main": []},
+                alignedAminoAcidSequences={},
+                aminoAcidInsertions={},
+            ),
+            errors=[
+                ProcessingAnnotation(
+                    source=[AnnotationSource(name=error[0], type=AnnotationSourceType.METADATA)],
+                    message=error[1],
+                )
+                for error in metadata_errors
+            ],
+            warnings=[
+                ProcessingAnnotation(
+                    source=[AnnotationSource(name=warning[0], type=AnnotationSourceType.METADATA)],
+                    message=warning[1],
+                )
+                for warning in metadata_warnings
+            ],
+        )

preprocessing/nextclade/src/loculus_preprocessing/prepro.py

@@ -625,7 +625,7 @@ def process_single(
                 ProcessingAnnotation(
                     source=[
                         AnnotationSource(
-                            name="main",
+                            name=output_field,
                             type=AnnotationSourceType.METADATA,
                         )
                     ],