Introduction

Suppose you have a file named somedata.csv that contains 12 columns of data in comma-separated values (CSV) format. From this file you want to extract only columns 2, 11, 5, and 9, and use them to create database records in a MySQL table that contains name, birth, height, and weight columns. You need to make sure that the height and weight are positive integers, and convert the birth dates from MM/DD/YY format to CCYY-MM-DD format. How can you do this?

In one sense, that problem is very specialized. But in another, it's not at all atypical, because data transfer problems with specific requirements occur frequently when transferring data into MySQL. It would be nice if datafiles were always nicely formatted and ready to load into MySQL with no preparation, but that is frequently not so. As a result, it's often necessary to preprocess information to put it into a format that MySQL finds acceptable. The reverse also is true; data exported from MySQL may need massaging to be useful for other programs.

Some data transfer operations are so difficult that they require a great deal of hand checking and reformatting, but in most cases, you can do at least part of the job automatically. Virtually all transfer problems involve at least some elements of a common set of conversion issues. This chapter discusses what these issues are, how to deal with them by taking advantage of the existing tools at your disposal, and how to write your own tools when necessary. The idea is not to cover all possible import and export situations (an impossible task), but to show some representative techniques and utilities, You can use them as is, or adapt them for problems that they don't handle. (There are also commercial conversion tools that may assist you, but my purpose here is to help you do things yourself.)

The first recipes in the chapter cover MySQL's native facilities for importing data (the LOAD DATA statement and the mysqlimport command-line program), and for exporting data (the SELECT ... INTO OUTFILE statement and the mysqldump program). For operations that don't require any data validation or reformatting, these facilities often are sufficient.

For situations where MySQL's native import and export capabilities do not suffice, the chapter moves on to cover techniques for using external supporting utilities and for writing your own. To some extent, you can avoid writing your own tools by using existing programs. For example, cut can extract columns from a file, and sed and tr can be used as postprocessors to convert query output into other formats. But you'll probably eventually reach the point where you decide to write your own programs. When you do, there are two broad sets of issues to consider:

  • How to manipulate the structure of datafiles. When a file is in a format that isn't suitable for import, you'll need to convert it to a different format. This many involve issues such as changing the column delimiters or line-ending sequences, or removing or rearranging columns in the file.
  • How to manipulate the content of datafiles. If you don't know whether the values contained in a file are legal, you may want to preprocess it to check or reformat them. Numeric values may need to be verified as lying within a specific range, dates may need to be converted to or from ISO format, and so forth.

Source code for the program fragments and scripts discussed in this chapter is located in the transfer directory of the recipes distribution, with the exception that some of the utility functions are contained in library files located in the lib directory. The code for some of the shorter utilities is shown in full. For the longer ones, the chapter generally discusses only how they work and how to use them, but you have access to the source if you wish to investigate in more detail how they're written.

The problems addressed in this chapter involve a lot of text processing and pattern matching. These are particular strengths of Perl, so the program fragments and utilities shown here are written mainly in Perl. PHP and Python provide pattern-matching capabilities, too, so they can of course do many of the same things. If you want to adapt the techniques described here for Java, you'll need to get a library that provides classes for regular expression-based pattern matching. See Appendix A for suggestions.

10.1.1 General Import and Export Issues

Incompatible datafile formats and differing rules for interpreting various kinds of values lead to many headaches when transferring data between programs. Nevertheless, certain issues recur frequently. By being aware of them, you'll be able to identify more easily just what you need to do to solve particular import or export problems.

In its most basic form, an input stream is just a set of bytes with no particular meaning. Successful import into MySQL requires being able to recognize which bytes represent structural information, and which represent the data values framed by that structure. Because such recognition is key to decomposing the input into appropriate units, the most fundamental import issues are these:

  • What is the record separator? Knowing this allows the input stream to be partitioned into records.
  • What is the field delimiter? Knowing this allows each record to be partitioned into field values. Recovering the original data values also may include stripping off quotes from around the values or recognizing escape sequences within them.

The ability to break apart the input into records and fields is important for extracting the data values from it. However, the values still might not be in a form that can be used directly, and you may need to consider other issues:

  • Do the order and number of columns match the structure of the database table? Mismatches require columns to be rearranged or skipped.
  • Do data values need to be validated or reformatted? If the values are in a format that matches MySQL's expectations, no further processing is necessary. Otherwise, they need to be checked and possibly rewritten.
  • How should NULL or empty values be handled? Are they allowed? Can NULL values even be detected? (Some systems export NULL values as empty strings, making it impossible to distinguish one from the other.)

For export from MySQL, the issues are somewhat the reverse. You probably can assume that values stored in the database are valid, but they may require reformatting, and it's necessary to add column and record delimiters to form an output stream that has a structure another program can recognize.

The chapter deals with these issues primarily within the context of performing bulk transfers of entire files, but many of the techniques discussed here can be applied in other situations as well. Consider a web-based application that presents a form for a user to fill in, then processes its contents to create a new record in the database. That is a data import situation. Web APIs generally make form contents available as a set of already-parsed discrete values, so the application may not need to deal with record and column delimiters, On the other hand, validation issues remain paramount. You really have no idea what kind of values a user is sending your script, so it's important to check them.

10.1.2 File Formats

Datafiles come in many formats, two of which are used frequently in this chapter:

  • Tab-delimited format. This is one of the simplest file structures; lines contain values separated by tab characters. A short tab-delimited file might look like this, where the whitespace between column values represents single tab characters:

    a b c
    a,b,c d e f
  • Comma-separated values (CSV) format. Files written in CSV format vary somewhat, because there is apparently no actual standard describing the format. However, the general idea is that lines consist of values separated by commas, and values containing internal commas are surrounded by quotes to prevent the commas from being interpreted as value delimiters. It's also common for values containing spaces to be quoted as well. Here is an example, where each line contains three values:

    a,b,c
    "a,b,c","d e",f

    It's trickier to process CSV files than tab-delimited files, because characters like quotes and commas have a dual meaning: they may represent file structure or be part of data values.

Another important datafile characteristic is the line-ending sequence. The most common sequences are carriage returns, linefeeds, and carriage return/linefeed pairs, sometimes referred to here by the abbreviations CR, LF, and CRLF.

Datafiles often begin with a row of column labels. In fact, a CSV file that begins with a row of names is what FileMaker Pro refers to as merge format. For some import operations, the row of labels is an annoyance because you must discard it to avoid having the labels be loaded into your table as a data record. But in other cases, the labels are quite useful:

  • For import into existing tables, the labels can be used to match up datafile columns with the table columns if they are not necessarily in the same order.
  • The labels can be used for column names when creating a new table automatically or semi-automatically from a datafile. For example, Recipe 10.37 later in the chapter discusses a utility that examines a datafile and guesses the CREATE TABLE statement that should be used to create a table from the file. If a label row is present, the utility uses them for column names. Otherwise, it's necessary to make up generic names like c1, c2, and so forth, which isn't very descriptive.

Tab Delimited, Linefeed Terminated Format

Although datafiles may be written in many formats, it's unlikely that you'll want to include machinery for reading several different formats within each file-processing utility that you write. I don't want to, either, so for that reason, many of the utilities described in this chapter assume for simplicity that their input is in tab-delimited, linefeed-terminated format. (This is also the default format for MySQL's LOAD DATA statement.) By making this assumption, it becomes easier to write programs that read files.

On the other hand, something has to be able to read data in other formats. To handle that problem, we'll develop a cvt_file.pl script that can read or write several types of files. (See Recipe 10.19.) The script is based on the Perl Text::CSV_XS module, which despite its name can be used for more than just CSV data. cvt_file.pl can convert between many file types, making it possible for other programs that require tab-delimited lines to be used with files not originally written in that format.

10.1.3 Notes on Invoking Shell Commands

This chapter shows a number of programs that you invoke from the command line using a shell like bash or tcsh under Unix or CMD.EXE ("the DOS prompt") under Windows. Many of the example commands for these programs use quotes around option values, and sometimes an option value is itself a quote character. Quoting conventions vary from one shell to another, but rules that seem to work with most of them (including CMD.EXE under Windows) are as follows:

  • For an argument that contains spaces, surround it with double quotes to prevent the shell from interpreting it as multiple separate arguments. The shell will strip off the quotes, then pass the argument to the command intact.
  • To include a double quote character in the argument itself, precede it with a backslash.

Some shell commands are so long that they're shown as you would enter them using several lines, with a backslash character as the line-continuation character:

% prog_name 
 argument1 
 argument2 ...

That works for Unix, but not for Windows, where you'll need to omit the continuation characters and type the entire command on one line:

C:> prog_name argument1 argument2 ...

Using the mysql Client Program

Writing MySQL-Based Programs

Record Selection Techniques

Working with Strings

Working with Dates and Times

Sorting Query Results

Generating Summaries

Modifying Tables with ALTER TABLE

Obtaining and Using Metadata

Importing and Exporting Data

Generating and Using Sequences

Using Multiple Tables

Statistical Techniques

Handling Duplicates

Performing Transactions

Introduction to MySQL on the Web

Incorporating Query Resultsinto Web Pages

Processing Web Input with MySQL

Using MySQL-Based Web Session Management

Appendix A. Obtaining MySQL Software

Appendix B. JSP and Tomcat Primer

Appendix C. References



MySQL Cookbook
MySQL Cookbook
ISBN: 059652708X
EAN: 2147483647
Year: 2005
Pages: 412
Authors: Paul DuBois

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