Small fixes, only insdcAccessionFull is shown on webpage - update to …

…also add this.

ena-submission/scripts/create_assembly.py

@@ -108,7 +108,7 @@ def get_segment_order(unaligned_sequences) -> list[str]:
                 segment_order.append(segment_name)
     else:
         segment_order.append("main")
-    return segment_order
+    return sorted(segment_order)
 
 
 def create_manifest_object(

ena-submission/scripts/ena_submission_helper.py

@@ -379,7 +379,7 @@ def check_ena(config: ENAConfig, erz_accession: str, segment_order: list[str]) -
 
     errors = []
     warnings = []
-    assembly_results = {}
+    assembly_results = {"segment_order": segment_order}
     try:
         response = requests.get(
             url,
@@ -419,20 +419,35 @@ def check_ena(config: ENAConfig, erz_accession: str, segment_order: list[str]) -
             if len(segment_order) == 1 and len(insdc_accession_range.split("-")) == 0:
                 assembly_results["insdc_accession"] = insdc_accession_range
             else:
-                insdc_accession_start_int = int(insdc_accession_range.split("-")[0][2:])
-                insdc_accession_end_int = int(insdc_accession_range.split("-")[-1][2:])
+                start_letters = insdc_accession_range.split("-")[0][:2]
+                start_digit = 10 ** (
+                    len(insdc_accession_range.split("-")[0]) - 2
+                )  # after letters accession can start with 0
+                insdc_accession_start_int = start_digit + int(
+                    insdc_accession_range.split("-")[0][2:]
+                )
+                insdc_accession_end_int = start_digit + int(
+                    insdc_accession_range.split("-")[-1][2:]
+                )
                 if insdc_accession_end_int - insdc_accession_start_int != len(segment_order) - 1:
                     logger.error(
                         "Unexpected response format: chromosome does not have expected number of segments"
                     )
                     raise requests.exceptions.RequestException
-                assembly_results.extend(
-                    {
-                        "insdc_accession_" + segment_order[i]: "OZ"
-                        + str(insdc_accession_start_int + i)
-                        for i in range(len(segment_order))
-                    }
-                )
+                insdc_accession_base_dict = {
+                    ("insdc_accession_" + segment): (
+                        start_letters + str(insdc_accession_start_int + i)[1:]
+                    )
+                    for i, segment in enumerate(segment_order)
+                }
+                insdc_accession_full_dict = {
+                    ("insdc_accession_full_" + segment): (
+                        start_letters + str(insdc_accession_start_int + i)[1:] + ".1"
+                    )
+                    for i, segment in enumerate(segment_order)
+                }  # set version to 1 by default
+                assembly_results.update(insdc_accession_base_dict)
+                assembly_results.update(insdc_accession_full_dict)
         else:
             return CreationResults(results=None, errors=errors, warnings=warnings)
     except:
@@ -443,7 +458,7 @@ def check_ena(config: ENAConfig, erz_accession: str, segment_order: list[str]) -
         logger.warning(error_message)
         errors.append(error_message)
         return CreationResults(results=None, errors=errors, warnings=warnings)
-    assembly_results.extend(
+    assembly_results.update(
         {
             "erz_accession": erz_accession,
             "gca_accession": gca_accession,

ena-submission/scripts/upload_external_metadata_to_loculus.py

@@ -86,13 +86,18 @@ def get_external_metadata(db_config: SimpleConnectionPool, entry: dict[str, Any]
             "gca_accession"
         ]
         insdc_accession_keys = [
-            key for key in corresponding_assembly[0]["result"] if key.startswith("insdc_accession")
+            key
+            for key in corresponding_assembly[0]["result"]
+            if key.startswith("insdc_accession_full")
         ]
-        segments = [key[len("insdc_accession") :] for key in insdc_accession_keys]
+        segments = [key[len("insdc_accession_full") :] for key in insdc_accession_keys]
         for segment in segments:
             data["externalMetadata"]["insdcAccessionBase" + segment] = corresponding_assembly[0][
                 "result"
             ]["insdc_accession" + segment]
+            data["externalMetadata"]["insdcAccessionFull" + segment] = corresponding_assembly[0][
+                "result"
+            ]["insdc_accession_full" + segment]
     else:
         raise Exception
     return data