Packages

•  package root

  Definition Classes

  root

•  package edu

  Definition Classes

  root

•  package chop

  Definition Classes

  edu

•  package cbmi

  Definition Classes

  chop

•  package dataExpress

  Definition Classes

  cbmi

•  package backends

  Provides database wrappers and connectivity for MySQL, Postgres, Oracle, and SQLite JDBC drivers.

  Provides database wrappers and connectivity for MySQL, Postgres, Oracle, and SQLite JDBC drivers.

  Overview

  The support for individual databases is broken out into several classes:

  • A edu.chop.cbmi.dataExpress.backends.SqlBackend which is the wrapper around the various JDBC method calls
  • A edu.chop.cbmi.dataExpress.backends.SqlDialect that contains the database-specific SQL quirks and implementation details
  • A edu.chop.cbmi.dataExpress.backends.SqlBackendProvider (optional) that allows a third-party backend to be supplied outside DataExpress

  The SqlBackend for the corresponding database is the primary means of establishing a datsbase connection when using DataExpress. However, It is important to note that it is generally easier, and safer to use the edu.chop.cbmi.dataExpress.backends.SqlBackendFactory to establish the necessary backend and set up the connection

  In general the SQLDialect and BackendProvider are used as part of a SQLBackend, and not directly.

  Usage

  The edu.chop.cbmi.dataExpress.backends.SqlBackend requires properties to fully configure itself. Typically these are loaded from a file, but can also be supplied through a standard java.util.Properties object. The SQL backend has very simple requirements for properties files. They must contain the following keys:

  • driverClassName: The class name for the actual database driver
  • jdbcUri: This is the URI required by the database driver. It is passed through directly to JDBC so you are free to specify schemas and other information here
  • username: The username to authenticate against the database (not required for non-authenticated RDBMS systems such as SQLite) -password: The password for accessing the database

  DataExpress will pass along any other properties it finds directly to JDBC, so in cases where a database requires specific connection configuration (e.g. to enable SSL for Postgres), those settings can be passed along.

  In some cases, DataExpress will set specific properties on the connection to ensure predictable behavior. Most of these have been empirically determined by our testing given the narrow use cases for DataExpress. Where possible, we have made it possible for you to override these defaults in your own configuration file, however this is generally not recommended.

  Definition Classes

  dataExpress

  Example:

  1. scala> import edu.chop.cbmi.dataExpress.backends._
     import edu.chop.cbmi.dataExpress.backends._
     
     scala> val backend = SqlBackendFactory "src/test/resources/sqlite_test.properties"
     backend: edu.chop.cbmi.dataExpress.backends.SqlBackend = SqlBackend({jdbcUri=jdbc:sqlite:target/source.sqlite},SqLiteDialect,org.sqlite.JDBC)
     
     scala> backend connect
     res0: java.sql.Connection = org.sqlite.Conn@7168f171
     
     scala> backend execute """CREATE TABLE de_test(id INTEGER, first_name VARCHAR, last_name VARCHAR)"""
     res1: Boolean = false
     
     scala> backend commit
     res3: Boolean = false
     
     scala> backend executeQuery "select count(*) from de_test"
     res4: java.sql.ResultSet = org.sqlite.RS@3b070e76
     
     scala> res4.getInt(1)
     res5: Int = 0

  Note

  The SQL backends return jdbc ResultSets which are typically a little more "low-level" than what you would probably want for ETL purporses. The edu.chop.cbmi.dataExpress.dataModels.sql.SqlRelation is a much more convenient object to use for ETL.

•  package file

  Definition Classes

  backends

• Append
• BooleanDelimiterMarshaller
• BooleanTypeFromRegex
• CustomMarshaller
• DateRegex
• DateTypeFromRegex
• DelimiterCustomMarshaller
• DelimiterMarshaller
• DoubleDelimiterMarshaller
• FileBackend
• FloatRegex
• FloatTypeFromRegex
• HeaderRowColumnNames
• IntDelimiterMarshaller
• IntTypeFromRegex
• KnownRegex
• MagicContainer
• MagicMarshaller
• MagicOptions
• Marshaller
• Overwrite
• StaticMarshaller
• TextFileBackend
• TextIterator
• TextTypeFromRegex
• TypeFromRegex
• TypedDelimiterMarshaller
• VarCharTypeFromRegex
• WriteMode
• WriteModeException

edu.chop.cbmi.dataExpress.backends.file

DelimiterCustomMarshaller 