Clean up tables

loculus-project · Jul 21, 2024 · 1b95382 · 1b95382
1 parent 66a7fbe
commit 1b95382
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git 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
@@ -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
@@ -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,