connect: connect

In OHDSI/DatabaseConnector: Connecting to Various Database Platforms

connect

Description

Creates a connection to a database server .There are four ways to call this function:

• connect(dbms, user, password, server, port, extraSettings, oracleDriver, pathToDriver)

• connect(connectionDetails)

• ⁠connect(dbms, connectionString, pathToDriver))⁠

• connect(dbms, connectionString, user, password, pathToDriver)

DBMS parameter details:

Depending on the DBMS, the function arguments have slightly different interpretations:

Oracle:

• user. The user name used to access the server

• password. The password for that user

• server. This field contains the SID, or host and servicename, SID, or TNSName: 'sid', 'host/sid', 'host/service name', or 'tnsname'

• port. Specifies the port on the server (default = 1521)

• extraSettings. The configuration settings for the connection (i.e. SSL Settings such as "(PROTOCOL=tcps)")

• oracleDriver. The driver to be used. Choose between "thin" or "oci".

• pathToDriver. The path to the folder containing the Oracle JDBC driver JAR files.

Microsoft SQL Server:

• user. The user used to log in to the server. If the user is not specified, Windows Integrated Security will be used, which requires the SQL Server JDBC drivers to be installed (see details below).

• password. The password used to log on to the server

• server. This field contains the host name of the server

• port. Not used for SQL Server

• extraSettings. The configuration settings for the connection (i.e. SSL Settings such as "encrypt=true; trustServerCertificate=false;")

• pathToDriver. The path to the folder containing the SQL Server JDBC driver JAR files.

Microsoft PDW:

• user. The user used to log in to the server. If the user is not specified, Windows Integrated Security will be used, which requires the SQL Server JDBC drivers to be installed (see details below).

• password. The password used to log on to the server

• server. This field contains the host name of the server

• port. Not used for SQL Server

• extraSettings. The configuration settings for the connection (i.e. SSL Settings such as "encrypt=true; trustServerCertificate=false;")

• pathToDriver. The path to the folder containing the SQL Server JDBC driver JAR files.

PostgreSQL:

• user. The user used to log in to the server

• password. The password used to log on to the server

• server. This field contains the host name of the server and the database holding the relevant schemas: host/database

• port. Specifies the port on the server (default = 5432)

• extraSettings. The configuration settings for the connection (i.e. SSL Settings such as "ssl=true")

• pathToDriver. The path to the folder containing the PostgreSQL JDBC driver JAR files.

Redshift:

• user. The user used to log in to the server

• password. The password used to log on to the server

• server. This field contains the host name of the server and the database holding the relevant schemas: host/database

• port. Specifies the port on the server (default = 5439)

• 'extraSettings The configuration settings for the connection (i.e. SSL Settings such as "ssl=true&sslfactory=com.amazon.redshift.ssl.NonValidatingFactory")

• pathToDriver. The path to the folder containing the RedShift JDBC driver JAR files.

Netezza:

• user. The user used to log in to the server

• password. The password used to log on to the server

• server. This field contains the host name of the server and the database holding the relevant schemas: host/database

• port. Specifies the port on the server (default = 5480)

• extraSettings. The configuration settings for the connection (i.e. SSL Settings such as "ssl=true")

• pathToDriver. The path to the folder containing the Netezza JDBC driver JAR file (nzjdbc.jar).

Impala:

• user. The user name used to access the server

• password. The password for that user

• server. The host name of the server

• port. Specifies the port on the server (default = 21050)

• extraSettings. The configuration settings for the connection (i.e. SSL Settings such as "SSLKeyStorePwd=*****")

• pathToDriver. The path to the folder containing the Impala JDBC driver JAR files.

SQLite:

• server. The path to the SQLIte file.

Spark / Databricks:

Currently both JDBC and ODBC connections are supported for Spark. Set the connectionString argument to use JDBC, otherwise ODBC is used:

• connectionString. The JDBC connection string (e.g. something like 'jdbc:databricks://my-org.cloud.databricks.com:443/default;transportMode=http;ssl=1;AuthMech=3;httpPath=/sql/1.0/warehouses/abcde12345;').

• user. The user name used to access the server. This can be set to 'token' when using a personal token (recommended).

• password. The password for that user. This should be your personal token when using a personal token (recommended).

• server. The host name of the server (when using ODBC), e.g. 'my-org.cloud.databricks.com')

• port. Specifies the port on the server (when using ODBC)

• extraSettings. Additional settings for the ODBC connection, for example extraSettings = list(HTTPPath = "/sql/1.0/warehouses/abcde12345", SSL = 1, ThriftTransport = 2, AuthMech = 3)

Snowflake:

• connectionString. The connection string (e.g. starting with 'jdbc:snowflake://host:port/?db=database').

• user. The user name used to access the server.

• password. The password for that user.

Windows authentication for SQL Server:

To be able to use Windows authentication for SQL Server (and PDW), you have to install the JDBC driver. Download the version 9.2.0 .zip from Microsoft and extract its contents to a folder. In the extracted folder you will find the file sqljdbc_9.2/enu/auth/x64/mssql-jdbc_auth-9.2.0.x64.dll (64-bits) or ssqljdbc_9.2/enu/auth/x86/mssql-jdbc_auth-9.2.0.x86.dll (32-bits), which needs to be moved to location on the system path, for example to c:/windows/system32. If you not have write access to any folder in the system path, you can also specify the path to the folder containing the dll by setting the environmental variable PATH_TO_AUTH_DLL, so for example Sys.setenv("PATH_TO_AUTH_DLL" = "c:/temp") Note that the environmental variable needs to be set before calling connect() for the first time.

Arguments

connectionDetails	An object of class connectionDetails as created by the createConnectionDetails() function.
dbms	The type of DBMS running on the server. Valid values are "oracle" for Oracle "postgresql" for PostgreSQL "redshift" for Amazon Redshift "sql server" for Microsoft SQL Server "pdw" for Microsoft Parallel Data Warehouse (PDW) "netezza" for IBM Netezza "bigquery" for Google BigQuery "sqlite" for SQLite "sqlite extended" for SQLite with extended types (DATE and DATETIME) "spark" for Spark "snowflake" for Snowflake
user	The user name used to access the server.
password	The password for that user.
server	The name of the server.
port	(optional) The port on the server to connect to.
extraSettings	(optional) Additional configuration settings specific to the database provider to configure things as security for SSL. For connections using JDBC these will be appended to end of the connection string. For connections using DBI, these settings will additionally be used to call dbConnect().
oracleDriver	Specify which Oracle drive you want to use. Choose between "thin" or "oci".
connectionString	The JDBC connection string. If specified, the server, port, extraSettings, and oracleDriver fields are ignored. If user and password are not specified, they are assumed to already be included in the connection string.
pathToDriver	Path to a folder containing the JDBC driver JAR files. See downloadJdbcDrivers() for instructions on how to download the relevant drivers.

Details

This function creates a connection to a database.

Value

An object that extends DBIConnection in a database-specific manner. This object is used to direct commands to the database engine.

Examples

## Not run: 
connectionDetails <- createConnectionDetails(
  dbms = "postgresql",
  server = "localhost/postgres",
  user = "root",
  password = "xxx"
)
conn <- connect(connectionDetails)
dbGetQuery(conn, "SELECT COUNT(*) FROM person")
disconnect(conn)

conn <- connect(dbms = "sql server", server = "RNDUSRDHIT06.jnj.com")
dbGetQuery(conn, "SELECT COUNT(*) FROM concept")
disconnect(conn)

conn <- connect(
  dbms = "oracle",
  server = "127.0.0.1/xe",
  user = "system",
  password = "xxx",
  pathToDriver = "c:/temp"
)
dbGetQuery(conn, "SELECT COUNT(*) FROM test_table")
disconnect(conn)

conn <- connect(
  dbms = "postgresql",
  connectionString = "jdbc:postgresql://127.0.0.1:5432/cmd_database"
)
dbGetQuery(conn, "SELECT COUNT(*) FROM person")
disconnect(conn)

## End(Not run)

OHDSI/DatabaseConnector documentation built on Jan. 31, 2024, 7:28 p.m.