Question

I am reading in some raw files and inserting them into a DB. This will involve MILLIONS of records, and for each record, I have multiple inserts (many tables). When I was testing locally, it was going quickly, but for the whole dataset, I need to work with a remote database. It is painfully slow this way, which I assume is because of all the trips over the network to delete/insert.

I am using the MySQLdb module (python) and at the moment, I have things such as the following:

# setup connection
con = mdb.connect('remote.host', 'database_user', '123456789', 'database_name');

... read files, loop through records, etc...

# clear out data related to current record
cur.execute("DELETE FROM articles WHERE article_id = %s", article.id)
cur.execute("DELETE FROM authors WHERE article_id = %s", article.id)
cur.execute("DELETE FROM addresses WHERE article_id = %s", article.id)
cur.execute("DELETE FROM citation_references WHERE article_id = %s", article.id)
cur.execute("DELETE FROM citation_patents WHERE article_id = %s", article.id)

# insert the article
cur.execute("INSERT INTO articles (article_id, doctype, keywords, language, title) VALUES (%s, %s, %s, %s, %s, %s)" , (article.id, article.doctype, ';'.join(article.keywords), article.language, article.title))

# insert all the authors
for au in article.authors:
    cur.execute("INSERT INTO isi_authors (article_id, name_first, name_last, email) VALUES (%s, %s, %s, %s)", (article.id, au.first_name, au.last_name, au.email))

... other loops like the authors to insert 10-20 citations per article, multiple addresses, etc ...

From what I can tell, MySQLdb does not allow me to send multiple queries at once. There must be a way for me to avoid the network delays. Any ideas?

Answer 1

Use executemany. Here’s an example from the manual:

c.executemany(
      """INSERT INTO breakfast (name, spam, eggs, sausage, price)
      VALUES (%s, %s, %s, %s, %s)""",
      [
      ("Spam and Sausage Lover's Plate", 5, 1, 8, 7.95 ),
      ("Not So Much Spam Plate", 3, 2, 0, 3.95 ),
      ("Don't Wany ANY SPAM! Plate", 0, 4, 3, 5.95 )
      ] )

In your case it would look something like this:

sql = "INSERT INTO isi_authors (article_id, name_first, name_last, email) VALUES (%s, %s, %s, %s)"
params = [(article.id, au.first_name, au.last_name, au.email) for au in article.authors]
cur.executemany(sql, params)

From the documentation of executemany:

This method improves performance on multiple-row INSERT and
REPLACE. Otherwise it is equivalent to looping over args with
execute().