Chromosomes must be named and unaligned sequences cannot include '-' …

…characters.

ena-submission/config/config.yaml

@@ -76,11 +76,11 @@ organisms:
       - externalMetadataUpdater: ena
         name: sraRunAccession
         type: string
-  ebola-sudan:
+  ebola-zaire:
     ingest:
-      taxon_id: 3052460
-      scientific_name: "Orthoebolavirus sudanense"
-    organismName: "Ebola Sudan"
+      taxon_id: 186538
+      scientific_name: "Orthoebolavirus zairense"
+    organismName: "Ebola Zaire"
     externalMetadata:
       - externalMetadataUpdater: ena
         name: ncbiReleaseDate

ena-submission/scripts/create_assembly.py

@@ -89,7 +89,7 @@ def create_chromosome_list_object(
     else:
         entry = AssemblyChromosomeListFileObject(
             object_name=f"{seq_key["accession"]}.{seq_key["version"]}",
-            chromosome_name="",
+            chromosome_name="main",
             chromosome_type=chromosome_type,
         )
         entries.append(entry)
@@ -464,7 +464,6 @@ def assembly_table_handle_errors(
             f"{config.backend_url}: ENA Submission pipeline found {len(entries_with_errors)} entries"
             f" in assembly_table in status HAS_ERRORS or SUBMITTING for over {time_threshold}m"
         )
-        logger.warning(error_msg)
         send_slack_notification(
             error_msg,
             slack_config,
@@ -482,7 +481,6 @@ def assembly_table_handle_errors(
             f"ENA Submission pipeline found {len(entries_waiting)} entries in assembly_table in"
             f" status WAITING for over {time_threshold_waiting}h"
         )
-        logger.warning(error_msg)
         send_slack_notification(
             config, error_msg, time=datetime.now(tz=pytz.utc), time_threshold=slack_time_threshold
         )

ena-submission/scripts/ena_submission_helper.py

@@ -258,11 +258,13 @@ def create_fasta(
         if len(unaligned_sequences.keys()) == 1:
             entry = chromosome_list.chromosomes[0]
             gz.write(f">{entry.object_name}\n".encode())
-            gz.write(f"{unaligned_sequences["main"]}\n".encode())
+            gz.write(f"{unaligned_sequences["main"].replace('-', 'N')}\n".encode())
         else:
             for entry in chromosome_list.chromosomes:
                 gz.write(f">{entry.object_name}\n".encode())
-                gz.write(f"{unaligned_sequences[entry.chromosome_name]}\n".encode())
+                gz.write(
+                    f"{unaligned_sequences[entry.chromosome_name].replace('-', 'N')}\n".encode()
+                )
 
     return filename
 

ena-submission/scripts/test_ena_submission.py

@@ -164,9 +164,28 @@ def test_sample_set_construction(self):
 
 class AssemblyCreationTests(unittest.TestCase):
     def setUp(self):
-        self.unaligned_sequences = sample_data_in_submission_table["unaligned_nucleotide_sequences"]
+        self.unaligned_sequences_multi = sample_data_in_submission_table[
+            "unaligned_nucleotide_sequences"
+        ]
+        self.unaligned_sequences = {
+            "main": "CTTAACTTTGAGAGAGTGAATT-",
+        }
         self.seq_key = {"accession": "test_accession", "version": "test_version"}
 
+    def test_create_chromosome_list_multi_segment(self):
+        chromosome_list = create_chromosome_list_object(
+            self.unaligned_sequences_multi, self.seq_key
+        )
+        file_name_chromosome_list = create_chromosome_list(chromosome_list)
+
+        with gzip.GzipFile(file_name_chromosome_list, "rb") as gz:
+            content = gz.read()
+
+        self.assertEqual(
+            content,
+            b"test_accession.test_version_seg2\tseg2\tlinear-segmented\ntest_accession.test_version_seg3\tseg3\tlinear-segmented\n",
+        )
+
     def test_create_chromosome_list(self):
         chromosome_list = create_chromosome_list_object(self.unaligned_sequences, self.seq_key)
         file_name_chromosome_list = create_chromosome_list(chromosome_list)
@@ -176,18 +195,32 @@ def test_create_chromosome_list(self):
 
         self.assertEqual(
             content,
-            b"test_accession.test_version_seg2\tseg2\tlinear-segmented\ntest_accession.test_version_seg3\tseg3\tlinear-segmented\n",
+            b"test_accession.test_version\tmain\tlinear-segmented\n",
+        )
+
+    def test_create_fasta_multi(self):
+        chromosome_list = create_chromosome_list_object(
+            self.unaligned_sequences_multi, self.seq_key
+        )
+        fasta_file_name = create_fasta(self.unaligned_sequences_multi, chromosome_list)
+
+        with gzip.GzipFile(fasta_file_name, "rb") as gz:
+            content = gz.read()
+        self.assertEqual(
+            content,
+            b">test_accession.test_version_seg2\nGCGGCACGTCAGTACGTAAGTGTATCTCAAAGAAATACTTAACTTTGAGAGAGTGAATT\n>test_accession.test_version_seg3\nCTTAACTTTGAGAGAGTGAATT\n",
         )
 
     def test_create_fasta(self):
+        # Also check that - is converted to N
         chromosome_list = create_chromosome_list_object(self.unaligned_sequences, self.seq_key)
         fasta_file_name = create_fasta(self.unaligned_sequences, chromosome_list)
 
         with gzip.GzipFile(fasta_file_name, "rb") as gz:
             content = gz.read()
         self.assertEqual(
             content,
-            b">test_accession.test_version_seg2\nGCGGCACGTCAGTACGTAAGTGTATCTCAAAGAAATACTTAACTTTGAGAGAGTGAATT\n>test_accession.test_version_seg3\nCTTAACTTTGAGAGAGTGAATT\n",
+            b">test_accession.test_version\nCTTAACTTTGAGAGAGTGAATTN\n",
         )
 
     def test_create_manifest(self):