read-lab-metadata: keep submitting_institution_id from metadata in EQA initial-config

CHANGELOG.md

@@ -32,6 +32,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Restore formatting and validation behavior after header reordering + add Excel warnings for MEPRAM [#856] (https://github.com/BU-ISCIII/relecov-tools/pull/856)
 - Adapted github actions workflows to load extra_config first [#863](https://github.com/BU-ISCIII/relecov-tools/pull/863)
 - Fix missing env vars in test_upload_validate step for test_sftp_modules [#866](https://github.com/BU-ISCIII/relecov-tools/pull/866)
+- read-lab-metadata: keep submitting_institution_id from metadata in EQA initial-config [#868](https://github.com/BU-ISCIII/relecov-tools/pull/868)
 
 #### Changed
 

relecov_tools/conf/initial_config-EQA2026.yaml

@@ -80,6 +80,7 @@ read_lab_metadata:
   lab_metadata_req_json: {}
   json_enrich:
     on_missing_schema_field: warn
+  force_submitting_institution_id_from_lab_code: false
   required_copy_from_other_field: {}
   samples_json_fields:
   - sequence_file_R1_md5

relecov_tools/read_lab_metadata.py

@@ -152,6 +152,11 @@ def __init__(
         self.required_post_processing = (
             self.project_config.get("required_post_processing", {}) or {}
         )
+        self.force_submitting_institution_id_from_lab_code = bool(
+            self.project_config.get(
+                "force_submitting_institution_id_from_lab_code", True
+            )
+        )
         self.json_req_files = self.project_config.get("lab_metadata_req_json", {}) or {}
         self.schema_name = self.relecov_sch_json["title"]
         self.schema_version = self.relecov_sch_json["version"]
@@ -499,7 +504,10 @@ def adding_fixed_fields(self, m_data):
                 m_data[idx]["schema_name"] = self.schema_name
             if "schema_version" in self.schema_property_names:
                 m_data[idx]["schema_version"] = self.schema_version
-            if "submitting_institution_id" in self.schema_property_names:
+            if (
+                "submitting_institution_id" in self.schema_property_names
+                and self.force_submitting_institution_id_from_lab_code
+            ):
                 m_data[idx]["submitting_institution_id"] = self.lab_code
         return m_data
 

relecov_tools/schema/relecov_schema_EQA.json

@@ -1536,6 +1536,7 @@
             "enum": [
                 "IRMA typing",
                 "INSaFLU",
+                "ABRicate",
                 "Custom typing script"
             ],
             "examples": [
@@ -1601,6 +1602,7 @@
             "enum": [
                 "IRMA subtyping",
                 "INSaFLU",
+                "ABRicate",
                 "Custom subtyping script"
             ],
             "examples": [