From d0be4cad6fa40992e042bd28c1177534ee160e7e Mon Sep 17 00:00:00 2001
From: "Anna (Anya) Parker" <50943381+anna-parker@users.noreply.github.com>
Date: Mon, 7 Oct 2024 12:09:36 +0200
Subject: [PATCH] update ena deposition pod with config changes

---
 ena-submission/scripts/create_project.py      | 4 ++--
 ena-submission/scripts/create_sample.py       | 4 ++--
 ena-submission/scripts/test_ena_submission.py | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/ena-submission/scripts/create_project.py b/ena-submission/scripts/create_project.py
index 437d037cd..f455158eb 100644
--- 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
index c0fec4844..c3c361d8f 100644
--- a/ena-submission/scripts/create_sample.py
+++ b/ena-submission/scripts/create_sample.py
@@ -132,7 +132,7 @@ 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)
@@ -140,7 +140,7 @@ def construct_sample_set_object(
     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
index 1bee66a27..e81596cfb 100644
--- 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"