From b1c6a420e131ce6c34c61e728525a408e64cab3b Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 26 Feb 2026 15:31:13 +0100 Subject: [PATCH 1/5] Add new enum to type/subtype_assignment_software_name --- relecov_tools/schema/relecov_schema_EQA.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/relecov_tools/schema/relecov_schema_EQA.json b/relecov_tools/schema/relecov_schema_EQA.json index b1a05566..958c8b1b 100644 --- a/relecov_tools/schema/relecov_schema_EQA.json +++ b/relecov_tools/schema/relecov_schema_EQA.json @@ -1536,6 +1536,7 @@ "enum": [ "IRMA typing", "INSaFLU", + "INSaFLU", "Custom typing script" ], "examples": [ @@ -1601,6 +1602,7 @@ "enum": [ "IRMA subtyping", "INSaFLU", + "ABRicate", "Custom subtyping script" ], "examples": [ From 8bdaf5445a190487933fb5ec1f16ff9cda4a1de4 Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 26 Feb 2026 15:31:53 +0100 Subject: [PATCH 2/5] Fix initial EQA2026 submitting_institution_id complete from path to xlsx --- relecov_tools/conf/initial_config-EQA2026.yaml | 1 + relecov_tools/read_lab_metadata.py | 10 +++++++++- 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/relecov_tools/conf/initial_config-EQA2026.yaml b/relecov_tools/conf/initial_config-EQA2026.yaml index b24220e8..a30c1470 100644 --- a/relecov_tools/conf/initial_config-EQA2026.yaml +++ b/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 diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index 1b2cafd8..aeb771eb 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/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 From 9943bf494a1691828d3d39b146fed09384d2d8ff Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 26 Feb 2026 15:34:57 +0100 Subject: [PATCH 3/5] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index f84613c2..e5e48a46 100755 --- a/CHANGELOG.md +++ b/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 From bb511381bd4282661f72abd7f2e9967ecb8bd5c2 Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 26 Feb 2026 15:40:25 +0100 Subject: [PATCH 4/5] Hotfix schema --- relecov_tools/schema/relecov_schema_EQA.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/relecov_tools/schema/relecov_schema_EQA.json b/relecov_tools/schema/relecov_schema_EQA.json index 958c8b1b..e7a97b16 100644 --- a/relecov_tools/schema/relecov_schema_EQA.json +++ b/relecov_tools/schema/relecov_schema_EQA.json @@ -1536,7 +1536,7 @@ "enum": [ "IRMA typing", "INSaFLU", - "INSaFLU", + "ABRicate", "Custom typing script" ], "examples": [ From 027b05e911ab3f59b1884065470ec43324e66838 Mon Sep 17 00:00:00 2001 From: Alejandro Date: Thu, 26 Feb 2026 15:52:17 +0100 Subject: [PATCH 5/5] Remove redundant boolean --- relecov_tools/read_lab_metadata.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/relecov_tools/read_lab_metadata.py b/relecov_tools/read_lab_metadata.py index aeb771eb..f3561d4d 100755 --- a/relecov_tools/read_lab_metadata.py +++ b/relecov_tools/read_lab_metadata.py @@ -152,10 +152,8 @@ 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.force_submitting_institution_id_from_lab_code = 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"]