From 018868b9cdfabf7dbb141e322fd6ec904ec08ba2 Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Wed, 22 May 2024 14:39:51 +0200
Subject: [PATCH] fix

---
 .../src/loculus_preprocessing/prepro.py       | 29 ++++++++++---------
 1 file changed, 15 insertions(+), 14 deletions(-)

diff --git a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
index 49069a80f7..39ea0e767a 100644
--- a/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
+++ b/preprocessing/nextclade/src/loculus_preprocessing/prepro.py
@@ -231,6 +231,7 @@ def process_single(
         "length": len(unprocessed.unalignedNucleotideSequences),
     }
 
+    alignment_failed = False
     for output_field, spec_dict in config.processing_spec.items():
         if output_field == "length":
             continue
@@ -241,7 +242,6 @@ def process_single(
             args=spec_dict.get("args", {}),
         )
         input_data: InputMetadata = {}
-        nextclade_failed = False
         for arg_name, input_path in spec.inputs.items():
             input_data[arg_name] = None
             # If field starts with "nextclade.", take from nextclade metadata
@@ -249,7 +249,7 @@ def process_single(
             if input_path.startswith(nextclade_prefix):
                 # Remove "nextclade." prefix
                 if unprocessed.nextcladeMetadata is None:
-                    nextclade_failed = True
+                    alignment_failed = True
                     continue
                 sub_path = input_path[len(nextclade_prefix) :]
                 input_data[arg_name] = str(
@@ -273,18 +273,6 @@ def process_single(
                 # )
                 continue
             input_data[arg_name] = unprocessed.inputMetadata[input_path]
-        if nextclade_failed:
-            errors.append(
-                ProcessingAnnotation(
-                    source=[
-                        AnnotationSource(
-                            name="main",
-                            type=AnnotationSourceType.NUCLEOTIDE_SEQUENCE,
-                        )
-                    ],
-                    message="Nucleotide sequence failed to align",
-                )
-            )
         processing_result = ProcessingFunctions.call_function(
             spec.function, spec.args, input_data, output_field
         )
@@ -298,6 +286,19 @@ def process_single(
             )
             output_metadata[output_field] = "Not provided"
 
+    if alignment_failed:
+        errors.append(
+            ProcessingAnnotation(
+                source=[
+                    AnnotationSource(
+                        name="main",
+                        type=AnnotationSourceType.NUCLEOTIDE_SEQUENCE,
+                    )
+                ],
+                message="Nucleotide sequence failed to align",
+            )
+        )
+
     logging.debug(f"Processed {id}: {output_metadata}")
 
     return ProcessedEntry(