Create an index on the metadata ID column

See docstring of db.load.sqlite3.create_metadata_index for reasoning.

augur/db/load/sqlite3.py

@@ -12,6 +12,7 @@ def load(metadata_file:str, metadata_table_name:str, db_file:str):
     database = Sqlite3Database(db_file)
 
     load_metadata(metadata, metadata_table_name, database)
+    create_metadata_index(metadata, metadata_table_name, database)
 
 
 def load_metadata(metadata:Metadata, table_name:str, database:Sqlite3Database):
@@ -37,3 +38,15 @@ def load_metadata(metadata:Metadata, table_name:str, database:Sqlite3Database):
         database.executemany(insert_statement, rows)
     except sqlite3.ProgrammingError:
         raise AugurError(f'Failed to load {metadata.file}.')
+
+
+def create_metadata_index(metadata:Metadata, table_name:str, database:Sqlite3Database):
+    """Create an index on the metadata ID column.
+
+    This serves to detect duplicates and speed up strain-based queries.
+    """
+    try:
+        database.create_unique_index(table_name, metadata.id_column)
+    except sqlite3.IntegrityError:
+        database.delete()
+        raise AugurError(f"Duplicate found in '{metadata.file}'.")

augur/io/sqlite3.py

@@ -37,6 +37,14 @@ def executemany(self, *args):
         with self.connect() as con:
             con.executemany(*args)
 
+    def create_unique_index(self, table_name:str, column:str):
+        """Create a unique index on a column in a table."""
+        index_name = f'index_{table_name}_{column}'
+        self.execute(f"""
+            CREATE UNIQUE INDEX {sanitize_identifier(index_name)}
+            ON {sanitize_identifier(table_name)} ({sanitize_identifier(column)})
+        """)
+
     def query_to_file(self, query:str, path:str, header=True, chunksize:int=10000, columns_to_exclude:List[str]=[], **to_csv_kwargs):
         """Query the database and write results to a tabular file.
 

tests/functional/db/cram/load-metadata-duplicates-error.t.err → tests/functional/db/cram/load-metadata-duplicates-error.t

@@ -14,3 +14,5 @@ Metadata with a duplicate under the ID column will error.
   $ ${AUGUR} db load \
   >  --metadata metadata.tsv \
   >  --to-sqlite3 data.sqlite3
+  ERROR: Duplicate found in 'metadata.tsv'.
+  [2]