Create an index on the metadata ID column

See docstring of db.import_.sqlite3.create_index for reasoning.

augur/db/import_/sqlite3.py

@@ -23,13 +23,15 @@ def import_(metadata_file:str, metadata_table_name:str,
             if bool(metadata_file and metadata_table_name):
                 metadata = Metadata(metadata_file)
                 import_metadata(metadata, metadata_table_name, database)
+                create_index(metadata.id_column, metadata_table_name, database)
 
             if sequences_file and sequences_table_name:
                 # Get ID column name from metadata if available.
                 id_column = metadata.id_column if bool(metadata_file and metadata_table_name) else DEFAULT_SEQUENCES_ID_COLUMN
 
                 sequences = Sequences(sequences_file)
                 import_sequences(sequences, id_column, sequences_table_name, database)
+                create_index(id_column, sequences_table_name, database)
         except Sqlite3ImportError as e:
             # Delete the database file if it was created for this import.
             if not db_file_existed:
@@ -80,3 +82,14 @@ def import_sequences(sequences:Sequences, id_column:str, table_name:str, databas
         database.executemany(insert_statement, records)
     except sqlite3.ProgrammingError as e:
         raise Sqlite3ImportError("Failed to import rows.") from e
+
+
+def create_index(column:str, table_name:str, database:Sqlite3Database):
+    """Create an index on a column.
+
+    This serves to detect duplicates and speed up strain-based queries.
+    """
+    try:
+        database.create_unique_index(table_name, column)
+    except sqlite3.IntegrityError:
+        raise Sqlite3ImportError(f"Duplicate found in column '{column}' of table '{table_name}'.")

augur/io/sqlite3.py

@@ -56,6 +56,14 @@ def create_table(self, table_name:str, columns:List[str]):
             )
         """)
 
+    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_csv(self, query:str, path:str, header=True, chunksize:int=10000, **to_csv_kwargs):
         """Query the database and write results to a tabular file.
 

tests/functional/db/cram/import-metadata-duplicates-error.t

@@ -0,0 +1,18 @@
+Setup
+
+  $ export AUGUR="$TESTDIR/../../../../bin/augur"
+
+Metadata with a duplicate under the ID column will error.
+
+  $ cat >metadata.tsv <<~~
+  > strain	date
+  > SEQ1	2000-01-01
+  > SEQ1	2000-02-01
+  > SEQ3	2000-03-01
+  > ~~
+
+  $ ${AUGUR} db import \
+  >  --metadata metadata.tsv \
+  >  --output-sqlite3 data.sqlite3
+  ERROR: Duplicate found in column 'strain' of table 'metadata'.
+  [2]