update ena deposition pod with config changes

loculus-project · Oct 7, 2024 · d0be4ca · d0be4ca
1 parent c827b39
commit d0be4ca
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/ena-submission/scripts/create_project.py b/ena-submission/scripts/create_project.py
@@ -73,13 +73,13 @@ def construct_project_set_object(
     Construct project set object, using:
     - entry in project_table
     - group_info of corresponding group_id
-    - config information, such as ingest metadata for that organism
+    - config information, such as enaDeposition metadata for that organism
 
     If test=True add a timestamp to the alias suffix to allow for multiple
     submissions of the same project for testing.
     (ENA blocks multiple submissions with the same alias)
     """
-    metadata_dict = config.organisms[entry["organism"]]["ingest"]
+    metadata_dict = config.organisms[entry["organism"]]["enaDeposition"]
     if test:
         alias = XmlAttribute(
             f"{entry["group_id"]}:{entry["organism"]}:{config.unique_project_suffix}:{datetime.now(tz=pytz.utc)}"

diff --git a/ena-submission/scripts/create_sample.py b/ena-submission/scripts/create_sample.py
@@ -132,15 +132,15 @@ def construct_sample_set_object(
     Construct sample set object, using:
     - entry in sample_table
     - sample_data_in_submission_table: corresponding entry in submission_table
-    - config information, such as ingest metadata for that organism
+    - config information, such as enaDeposition metadata for that organism
     If test=True add a timestamp to the alias suffix to allow for multiple
     submissions of the same project for testing.
     (ENA blocks multiple submissions with the same alias)
     """
     sample_metadata = sample_data_in_submission_table["metadata"]
     center_name = sample_data_in_submission_table["center_name"]
     organism = sample_data_in_submission_table["organism"]
-    organism_metadata = config.organisms[organism]["ingest"]
+    organism_metadata = config.organisms[organism]["enaDeposition"]
     if test:
         alias = XmlAttribute(
             f"{entry["accession"]}:{organism}:{config.unique_project_suffix}:{datetime.now(tz=pytz.utc)}"

diff --git a/ena-submission/scripts/test_ena_submission.py b/ena-submission/scripts/test_ena_submission.py
@@ -48,7 +48,7 @@ def mock_config():
         "scientific_name": "Test scientific name",
         "molecule_type": "genomic RNA",
     }
-    config.organisms = {"Test organism": {"ingest": metadata_dict}}
+    config.organisms = {"Test organism": {"enaDeposition": metadata_dict}}
     config.metadata_mapping = defaults["metadata_mapping"]
     config.metadata_mapping_mandatory_field_defaults = defaults[
         "metadata_mapping_mandatory_field_defaults"