File indexing (using Binary trees?) in Python

Question

Background

I have many (thousands!) of data files with a standard field based format (think tab-delimited, same fields in every line, in every file). I'm debating various ways of making this data available / searchable. (Some options include RDBMS, NoSQL stuff, using the grep/awk and friends, etc.).

Proposal

In particular, one idea that appeals to me is "indexing" the files in some way. Since these files are read-only (and static), I was imagining some persistent files containing binary trees (one for each indexed field, just like in other data stores). I'm open to ideas about how to this, or to hearing that this is simply insane. Mostly, my favorite search engine hasn't yielded me any pre-rolled solutions for this.

I realize this is a little ill-formed, and solutions are welcome.

Additional Details

• files long, not wide
  • millions of lines per hour, spread over 100 files per hour
  • tab seperated, not many columns (~10)
  • fields are short (say < 50 chars per field)
• queries are on fields, combinations of fields, and can be historical

Drawbacks to various solutions:

(All of these are based on my observations and tests, but I'm open to correction)

BDB

• has problems with scaling to large file sizes (in my experience, once they're 2GB or so, performance can be terrible)
• single writer (if it's possible to get around this, I want to see code!)
• hard to do multiple indexing, that is, indexing on different fields at once (sure you can do this by copying the data over and over).
• since it only stores strings, there is a serialize / deserialize step

RDBMSes

Wins:

• flat table model is excellent for querying, indexing

Losses:

• In my experience, the problem comes with indexing. From what I've seen (and please correct me if I am wrong), the issue with rdbmses I know (sqlite, postgres) supporting either batch load (then indexing is slow at the end), or row by row loading (which is low). Maybe I need more performance tuning.

Answer 1

Why reinvent the wheel? By all means, index the files, but use Whoosh, or Lucene, etc.

Edit: you hadn't stated your performance requirements at the time I posted this answer. You're not going to be able to index "millions of rows per hour" with off-the-shelf software.

Answer 2

The physical storage access time will tend to dominate anything you do. When you profile, you'll find that the read() is where you spend most of your time.

To reduce the time spent waiting for I/O, your best bet is compression.

Create a huge ZIP archive of all of your files. One open, fewer reads. You'll spend more CPU time. I/O time, however, will dominate your processing, so reduce I/O time by zipping everything.

Answer 3

If the data is already organized in fields, it doesn't sound like a text searching/indexing problem. It sounds like tabular data that would be well-served by a database.

Script the file data into a database, index as you see fit, and query the data in any complex way the database supports.

That is unless you're looking for a cool learning project. Then, by all means, come up with an interesting file indexing scheme.

Answer 4

There are a number of file-based DBMSes designed for the sort of data you describe. One of the most widely used is Berkeley DB. It's open source, now owned by Oracle, and comes in C and Java flavors (with Python and other language wrappers for the C version).

Since your data is read-only, though, there are other options. One that comes to mind is CDB. It likewise has Python interfaces, as well as a pure Python reimplementation.

Or, if you really like implementing things yourself, you could always implement SSTables from Google's Bigtable paper. ;)

Answer 5

sqlite3 is fast, small, part of python (so nothing to install) and provides indexing of columns. It writes to files, so you wouldn't need to install a database system.