From 963a7423112815830aa6659772589eb3b1445cd7 Mon Sep 17 00:00:00 2001 From: "Anna (Anya) Parker" <50943381+anna-parker@users.noreply.github.com> Date: Mon, 7 Oct 2024 17:27:09 +0200 Subject: [PATCH 1/5] Add address # Conflicts: # ena-submission/scripts/create_assembly.py --- ena-submission/scripts/create_assembly.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/ena-submission/scripts/create_assembly.py b/ena-submission/scripts/create_assembly.py index ab66c6c68..43cc4304f 100644 --- a/ena-submission/scripts/create_assembly.py +++ b/ena-submission/scripts/create_assembly.py @@ -7,6 +7,7 @@ import click import pytz import yaml +from call_loculus import get_group_info from ena_submission_helper import ( CreationResult, create_chromosome_list, @@ -134,6 +135,10 @@ def create_manifest_object( sample_accession = sample_table_entry["result"]["ena_sample_accession"] study_accession = project_table_entry["result"]["bioproject_accession"] + group_info = get_group_info(config, project_table_entry["group_id"])[0]["group"] + address = group_info["address"] + logger.debug(f"Creating manifest with address:{address}") + metadata = submission_table_entry["metadata"] unaligned_nucleotide_sequences = submission_table_entry["unaligned_nucleotide_sequences"] organism_metadata = config.organisms[group_key["organism"]]["enaDeposition"] @@ -205,6 +210,7 @@ def create_manifest_object( description=description, moleculetype=moleculetype, authors=authors, + address=address, ) From de384c243cb7883fadc91512af165d6c9f0651d2 Mon Sep 17 00:00:00 2001 From: "Anna (Anya) Parker" <50943381+anna-parker@users.noreply.github.com> Date: Mon, 7 Oct 2024 17:35:08 +0200 Subject: [PATCH 2/5] Fix address parsing --- ena-submission/scripts/create_assembly.py | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/ena-submission/scripts/create_assembly.py b/ena-submission/scripts/create_assembly.py index 43cc4304f..f6be9c99b 100644 --- a/ena-submission/scripts/create_assembly.py +++ b/ena-submission/scripts/create_assembly.py @@ -135,9 +135,15 @@ def create_manifest_object( sample_accession = sample_table_entry["result"]["ena_sample_accession"] study_accession = project_table_entry["result"]["bioproject_accession"] - group_info = get_group_info(config, project_table_entry["group_id"])[0]["group"] - address = group_info["address"] - logger.debug(f"Creating manifest with address:{address}") + try: + group_info = get_group_info(config, project_table_entry["group_id"])[0]["group"] + address = group_info["address"] + address_string = (f'{address.get("line1", "")}, {address.get("line2", "")}, ' + f'{address.get("city", "")}, {address.get("state", "")}, ' + f'{address.get("postalCode", "")}, {address.get("country")}') + except: + address_string = project_table_entry["center_name"] + logger.error("Was unable to create address, setting address to center_name") metadata = submission_table_entry["metadata"] unaligned_nucleotide_sequences = submission_table_entry["unaligned_nucleotide_sequences"] @@ -210,7 +216,7 @@ def create_manifest_object( description=description, moleculetype=moleculetype, authors=authors, - address=address, + address=address_string, ) From d34b5886b65ae9d756e6c42594611a12b4dbf002 Mon Sep 17 00:00:00 2001 From: "Anna (Anya) Parker" <50943381+anna-parker@users.noreply.github.com> Date: Mon, 7 Oct 2024 17:37:32 +0200 Subject: [PATCH 3/5] fix tests --- ena-submission/scripts/create_assembly.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/ena-submission/scripts/create_assembly.py b/ena-submission/scripts/create_assembly.py index f6be9c99b..fcd77bb14 100644 --- a/ena-submission/scripts/create_assembly.py +++ b/ena-submission/scripts/create_assembly.py @@ -135,15 +135,16 @@ def create_manifest_object( sample_accession = sample_table_entry["result"]["ena_sample_accession"] study_accession = project_table_entry["result"]["bioproject_accession"] - try: - group_info = get_group_info(config, project_table_entry["group_id"])[0]["group"] - address = group_info["address"] - address_string = (f'{address.get("line1", "")}, {address.get("line2", "")}, ' - f'{address.get("city", "")}, {address.get("state", "")}, ' - f'{address.get("postalCode", "")}, {address.get("country")}') - except: - address_string = project_table_entry["center_name"] - logger.error("Was unable to create address, setting address to center_name") + address_string = project_table_entry["center_name"] + if config.is_broker: + try: + group_info = get_group_info(config, project_table_entry["group_id"])[0]["group"] + address = group_info["address"] + address_string = (f'{address.get("line1", "")}, {address.get("line2", "")}, ' + f'{address.get("city", "")}, {address.get("state", "")}, ' + f'{address.get("postalCode", "")}, {address.get("country")}') + except: + logger.error("Was unable to create address, setting address to center_name") metadata = submission_table_entry["metadata"] unaligned_nucleotide_sequences = submission_table_entry["unaligned_nucleotide_sequences"] From 12a10e2374f08f85e49b4e136c90ca99049cbf37 Mon Sep 17 00:00:00 2001 From: "Anna (Anya) Parker" <50943381+anna-parker@users.noreply.github.com> Date: Mon, 7 Oct 2024 17:39:28 +0200 Subject: [PATCH 4/5] fix tests (cherry picked from commit 673786c33cdba1a2f490f50e1fd08e00de307ca8) --- ena-submission/scripts/test_ena_submission.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/ena-submission/scripts/test_ena_submission.py b/ena-submission/scripts/test_ena_submission.py index e81596cfb..9e2c1e211 100644 --- a/ena-submission/scripts/test_ena_submission.py +++ b/ena-submission/scripts/test_ena_submission.py @@ -240,7 +240,10 @@ def test_create_manifest(self): study_accession = "Test Study Accession" sample_accession = "Test Sample Accession" results_in_sample_table = {"result": {"ena_sample_accession": sample_accession}} - results_in_project_table = {"result": {"bioproject_accession": study_accession}} + results_in_project_table = { + "result": {"bioproject_accession": study_accession}, + "center_name": "generic_center_name", + } manifest = create_manifest_object( config, results_in_sample_table, From 47f81d0a897b1540d4953cfcf89030b9e1b93b26 Mon Sep 17 00:00:00 2001 From: "Anna (Anya) Parker" <50943381+anna-parker@users.noreply.github.com> Date: Mon, 7 Oct 2024 17:47:33 +0200 Subject: [PATCH 5/5] log error --- ena-submission/scripts/create_assembly.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ena-submission/scripts/create_assembly.py b/ena-submission/scripts/create_assembly.py index fcd77bb14..41718c4dc 100644 --- a/ena-submission/scripts/create_assembly.py +++ b/ena-submission/scripts/create_assembly.py @@ -143,8 +143,8 @@ def create_manifest_object( address_string = (f'{address.get("line1", "")}, {address.get("line2", "")}, ' f'{address.get("city", "")}, {address.get("state", "")}, ' f'{address.get("postalCode", "")}, {address.get("country")}') - except: - logger.error("Was unable to create address, setting address to center_name") + except Exception as e: + logger.error(f"Was unable to create address, setting address to center_name due to {e}") metadata = submission_table_entry["metadata"] unaligned_nucleotide_sequences = submission_table_entry["unaligned_nucleotide_sequences"]