diff --git a/ena-submission/flyway/sql/V1__Initial_Schema.sql b/ena-submission/flyway/sql/V1__Initial_Schema.sql index 6b8baeaa6..40ff4631b 100644 --- a/ena-submission/flyway/sql/V1__Initial_Schema.sql +++ b/ena-submission/flyway/sql/V1__Initial_Schema.sql @@ -31,7 +31,6 @@ CREATE TABLE project_table ( CREATE TABLE sample_table ( accession text not null, version bigint not null, - organism text not null, errors jsonb, warnings jsonb, status text not null, diff --git a/ena-submission/scripts/create_sample.py b/ena-submission/scripts/create_sample.py index 060ed089a..fcb1a96e0 100644 --- a/ena-submission/scripts/create_sample.py +++ b/ena-submission/scripts/create_sample.py @@ -144,7 +144,7 @@ def create_sample(log_level, config_file): ) else: # If not: create sample_entry, change status to SUBMITTING_SAMPLE - sample_table_entry = SampleTableEntry(**seq_key, center_name=row["center_name"]) + sample_table_entry = SampleTableEntry(**seq_key) add_to_sample_table(db_config, sample_table_entry) update_values = {"status_all": StatusAll.SUBMITTING_SAMPLE.name} number_rows_updated = update_db_where_conditions( @@ -196,13 +196,14 @@ def create_sample(log_level, config_file): f"Found {len(ready_to_submit_sample)} entries in sample_table in status READY" ) for row in ready_to_submit_sample: - organism_metadata = config.organisms[row["organism"]]["ingest"] seq_key = {"accession": row["accession"], "version": row["version"]} sample_data_in_submission_table = find_conditions_in_db( db_config, table_name="submission_table", conditions=seq_key ) sample_metadata = sample_data_in_submission_table[0]["metadata"] center_name = sample_data_in_submission_table[0]["center_name"] + organism = sample_data_in_submission_table[0]["organism"] + organism_metadata = config.organisms[organism]["ingest"] sample_set = construct_sample_set_object( config, organism_metadata, sample_metadata, center_name, row diff --git a/ena-submission/scripts/submission_db_helper.py b/ena-submission/scripts/submission_db_helper.py index 148e21e3f..40ebb7e28 100644 --- a/ena-submission/scripts/submission_db_helper.py +++ b/ena-submission/scripts/submission_db_helper.py @@ -92,7 +92,6 @@ class ProjectTableEntry: class SampleTableEntry: accession: str version: int - organism: str errors: str | None = None warnings: str | None = None status: Status = Status.READY @@ -208,11 +207,10 @@ def add_to_sample_table(db_config: DBConfig, sample_table_entry: SampleTableEntr sample_table_entry.started_at = datetime.now(tz=pytz.utc) cur.execute( - "insert into sample_table values(%s,%s,%s,%s,%s,%s,%s,%s,%s)", + "insert into sample_table values(%s,%s,%s,%s,%s,%s,%s,%s)", ( sample_table_entry.accession, sample_table_entry.version, - sample_table_entry.organism, sample_table_entry.errors, sample_table_entry.warnings, sample_table_entry.status.name,