Package 'ODB' reference manual

Title:	Open Document Databases (.odb) Management
Description:	Functions to create, connect, update and query 'HSQL' databases embedded in Open Document Databases files, as 'OpenOffice' and 'LibreOffice' do.
Authors:	Sylvain Mareschal
Maintainer:	Sylvain Mareschal <[email protected]>
License:	GPL (>= 3)
Version:	1.2.1
Built:	2024-11-15 06:41:33 UTC
Source:	CRAN

Open Document Databases (.odb) Management

Description

Functions to create, connect, update and query 'HSQL' databases embedded in Open Document Databases files, as 'OpenOffice' and 'LibreOffice' do.

Details

The DESCRIPTION file:

Package:	ODB
Type:	Package
Title:	Open Document Databases (.odb) Management
Version:	1.2.1
Date:	2020-03-10
Author:	Sylvain Mareschal
Maintainer:	Sylvain Mareschal <[email protected]>
URL:	http://bioinformatics.ovsa.fr/ODB
BugReports:	https://github.com/maressyl/R.ODB/issues
Description:	Functions to create, connect, update and query 'HSQL' databases embedded in Open Document Databases files, as 'OpenOffice' and 'LibreOffice' do.
License:	GPL (>= 3)
Depends:	methods, DBI, RJDBC
Imports:	utils
SystemRequirements:	zip
NeedsCompilation:	no
Packaged:	2020-03-11 11:44:12 UTC; sylvain
Repository:	CRAN
Date/Publication:	2020-03-11 12:40:08 UTC
Config/pak/sysreqs:	make default-jdk

Index of help topics:

ODB-class               Class "ODB"
ODB-package             Open Document Databases (.odb) Management
difftimeFmt             Formats a time difference in multiple units
isClosed                Checks if a DBI connection is closed
odb.close               Closes an "ODB" connection and updates the .odb
                        file
odb.comments            Gets or sets column comments in an ODB database
odb.create              Creates a .odb empty file.
odb.export              Exports an ODB database to a SQL file.
odb.insert              Wrapper for inserting data in an ODB table.
odb.open                Creates a connection to a .odb file
odb.queries             Gets or sets stored queries in an ODB database
odb.read                Executes a reading SQL query in an ODB database
                        (SELECT ...)
odb.tables              Gets description of every table in an ODB
                        database.
odb.write               Executes writing SQL queries in an ODB database
                        (INSERT ...)
progress-class          Classes "progress", "progress.file" and
                        "progress.console"

First notice this package is not intented to manage all .odb variations. Currently two distinct types of .odb files can be distinguished : files embedding an HSQL database, and files connecting to a remote database engine such as MySQL. This package is made for the formers, as remote databases can be queried directly using the DBI package. Functions involving the XML content of the .odb file (odb.comments and odb.queries) may be operative on such files, but there is no garantee they would be.

You should not consider this package without minimal knowledge of the SQL language, as only a few basic operations have functions not relying on the user to build a valid SQL query (odb.insert, odb.tables, odb.comments, odb.queries).

This package is built around the odb class, which extends DBIConnection. A set of functions is provided to execute reading (SELECT ...) or writing (INSERT, CREATE, DROP ...) SQL queries through the HSQLDB engine, and a set of convenient tools is also provided for the most common tasks (odb.read, odb.write, odb.insert). A few Open Document specific functions are also provided, allowing modifications on features provided by the .odb file format and not the database itself (odb.comments and odb.queries).

Effects of all these functions can be achieved manually via the OpenOffice or LibreOffice Base software, obviously this package offers a way of automating it on a bigger scale. Both manual and automatic modifications can be done on the same .odb file, but users are strongly recommended to not use the two methods simultaneously. This R package works on a copy of the file made at the odb.open call, and this copy will replace the original file at the odb.close call, regardless of what happened between the two calls.

Additional tools are also provided, notably odb.export and isClosed.

See the 'examples' section for more details on the package behavior.

Author(s)

Sylvain Mareschal

Maintainer: Sylvain Mareschal <[email protected]>

Examples


  ## CONNECTION ##
  
  # Creation of a new .odb database
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")

  # Connection to the file
  odb <- odb.open(odbFile)
  
  
  ## STRUCTURE ##
  
  # Creation of a new table
  SQL <- "CREATE TABLE fruits (id INTEGER PRIMARY KEY, value VARCHAR(8))"
  odb.write(odb, SQL)
  
  # Addition of comments on columns
  odb.comments(odb, "fruits", c("id", "value")) <- c("Fruit rank", "Fruit name")
  
  # Printing of the database structure
  print(odb.tables(odb))
  
  # Printing of a specific comment
  print(odb.comments(odb, "fruits", "value"))
  
  
  ## DATA ##
  
  # Insertion of data
  data <- data.frame(id=1:3, value=c("apple", "orange", "pear"))
  odb.insert(odb, tableName="fruits", data=data, execute=TRUE)
  
  # Reading
  print(odb.read(odb, "SELECT * FROM fruits WHERE id=2"))
  
  # Saved query
  odb.queries(odb, "2nd record") <- "SELECT * FROM fruits WHERE id=2"
  print(odb.read(odb, odb.queries(odb, "2nd record")))
  
  # SQL export
  sqlFile <- tempfile(fileext=".sql")
  odb.export(odb, sqlFile)
  
  
  ## DISCONNECTION ##
  
  # Is the connection closed ?
  print(isClosed(odb))
  
  # Save changes in the .odb file
  odb.close(odb, write=TRUE)
  
  # And now ?
  print(isClosed(odb))
## CONNECTION ##
  
  # Creation of a new .odb database
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")

  # Connection to the file
  odb <- odb.open(odbFile)
  
  
  ## STRUCTURE ##
  
  # Creation of a new table
  SQL <- "CREATE TABLE fruits (id INTEGER PRIMARY KEY, value VARCHAR(8))"
  odb.write(odb, SQL)
  
  # Addition of comments on columns
  odb.comments(odb, "fruits", c("id", "value")) <- c("Fruit rank", "Fruit name")
  
  # Printing of the database structure
  print(odb.tables(odb))
  
  # Printing of a specific comment
  print(odb.comments(odb, "fruits", "value"))
  
  
  ## DATA ##
  
  # Insertion of data
  data <- data.frame(id=1:3, value=c("apple", "orange", "pear"))
  odb.insert(odb, tableName="fruits", data=data, execute=TRUE)
  
  # Reading
  print(odb.read(odb, "SELECT * FROM fruits WHERE id=2"))
  
  # Saved query
  odb.queries(odb, "2nd record") <- "SELECT * FROM fruits WHERE id=2"
  print(odb.read(odb, odb.queries(odb, "2nd record")))
  
  # SQL export
  sqlFile <- tempfile(fileext=".sql")
  odb.export(odb, sqlFile)
  
  
  ## DISCONNECTION ##
  
  # Is the connection closed ?
  print(isClosed(odb))
  
  # Save changes in the .odb file
  odb.close(odb, write=TRUE)
  
  # And now ?
  print(isClosed(odb))

Formats a time difference in multiple units

Description

This function converts a time difference (in seconds) into a string with various time units (days, hours, minutes, seconds and milliseconds).

Usage

  difftimeFmt(x)
difftimeFmt(x)

Arguments

`x`	Time difference to format (single value). Can be a floating number of seconds, or a `difftime` object.

Value

Returns a character of length 1, according to the following format : "[d]d [h]:[m]:[s].[ms]". Days and milliseconds are omitted if they can be.

Author(s)

Sylvain Mareschal

Examples

  # Full format
  difftimeFmt(94521.125846)
  
  # With dates
  T1 <- strptime("2011-03-21 14:32:03", format="%Y-%m-%d %H:%M:%S")
  T2 <- strptime("2011-08-06 18:14:21", format="%Y-%m-%d %H:%M:%S")
  dT <- as.double(difftime(T2, T1, units="secs"))
  difftimeFmt(dT)
# Full format
  difftimeFmt(94521.125846)
  
  # With dates
  T1 <- strptime("2011-03-21 14:32:03", format="%Y-%m-%d %H:%M:%S")
  T2 <- strptime("2011-08-06 18:14:21", format="%Y-%m-%d %H:%M:%S")
  dT <- as.double(difftime(T2, T1, units="secs"))
  difftimeFmt(dT)

Checks if a DBI connection is closed

Description

Checks if a connection inheriting from the DBIConnection class (including 'ODB' connections) is closed.

Usage

  isClosed(connection)
isClosed(connection)

Arguments

connection

An object inheriting from DBIConnection class.

Value

Returns a single logical value, whether SQL queries can be sent to the connection or not.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  ODB <- odb.open(odbFile)
  
  # Is the connection closed ?
  print(isClosed(ODB))
  
  # Save changes in the .odb file
  odb.close(ODB, write=TRUE)
  
  # And now ?
  print(isClosed(ODB))
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  ODB <- odb.open(odbFile)
  
  # Is the connection closed ?
  print(isClosed(ODB))
  
  # Save changes in the .odb file
  odb.close(ODB, write=TRUE)
  
  # And now ?
  print(isClosed(ODB))

Class "ODB"

Description

A connection to an Open Document Base (.odb) embedded HSQL database.

This class extends JDBCConnection, and objects from it can be accessed via the DBI interface. Objects from this class also store file paths used for other ODB manipulation (such as queries or comments, stored in the embedded content.xml file rather than the HSQL database).

Objects from the Class

Objects can be created by calls to the odb.open function, and saved into the original .odb file by odb.close.

Several objects can but should not refer to the same .odb file: as they deal with distinct copies of this file, updates in one connection will not propagate to others. Moreover, when one of these connections will be closed, it will override changes in the .odb file made by formerly closed connections.

Slots

jc:: Inherited from "JDBCConnection"
identifier.quote:: Inherited from "JDBCConnection"
directory:: Single character value, the path to the temp directory storing the database files.
odbFile:: Single character value, the path to the .odb file handled.
odbVersion:: Single character value, HSQLDB version of the .odb file.
jarFile:: Single character value, the path to the HSQLDB .jar library used.
jarVersion:: Single character value, HSQLDB version of the .jar library.

Extends

Class "JDBCConnection", directly.
Class "DBIConnection", by class "JDBCConnection", distance 2.
Class "DBIObject", by class "JDBCConnection", distance 3.

Methods

show: signature(object = "ODB")

Note

Functions from the DBI package can be used directly on the object, if you prefer to manage SQL transactions yourself. Notice however that common issues (charset, factors and column names) are handled by odb.read and odb.write, which can deal with any SQL query.

Author(s)

Sylvain Mareschal

Closes an "ODB" connection and updates the .odb file

Description

Closes the connection to the embedded HSQLDB, removing temporary files and updating the .odb file if asked to do so.

Usage

  odb.close(odb, write = TRUE)
odb.close(odb, write = TRUE)

Arguments

`odb`	An `ODB` object, as produced by `odb.open`.
`write`	Single logical value, defining if the modifications has to be saved in the original .odb file or not. Notice they will be definitively lost if closing with write=FALSE.

Value

Invisibly returns TRUE if succeeds, raises an error if not.

Note

To take data in a first file and save it in an other, copy the file before using odb.open.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)

Gets or sets column comments in an ODB database

Description

This function allows comment manipulation into OpenOffice Base databases, through an odb connection.

Usage

  odb.comments(odb, tableNames = NULL, columnNames = NULL, simplify = TRUE)
  odb.comments(odb, tableNames, columnNames) <- value
odb.comments(odb, tableNames = NULL, columnNames = NULL, simplify = TRUE)
  odb.comments(odb, tableNames, columnNames) <- value

Arguments

`odb`	An `ODB` object, as produced by `odb.open`.
`tableNames`	Character vector naming tables to search comments in. See the 'Details' section.
`columnNames`	Character vector naming columns to search comments in. See the 'Details' section.
`simplify`	Single logical value, whether to simplify returns. See the 'Value' section
`value`	Character vector, the comments to store.

Details

tableNames, columnNames and value can be considered as columns from a same data.frame: the first comment considered will be the comment on the first columnNames for the first tableNames, and so on. Vectors are repeated to achieve same lengths if necessary.

The NULL value can be used for tableNames and columnNames in the first syntax, with the meaning of "all possible values". See the 'Examples' section.

Value

The first syntax returns a list of character vectors. Names in the list are table names, names in vectors are column names. Only tables and columns with comments are present in the results.

With simplify set to TRUE, a character vector is directly returned (without embedding list) when a single tableNames is interrogated, and column names are skipped if a single tableNames / columnNames couple is provided.

Note

Comments on non-existing tables or columns can be manipulated as well, as there is no link between the comment storage engine and the database itself. Keep in mind these comments are stored in the .odb file, not the database itself.

Comments can also be added manually from OpenOffice while creating a table.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  ODB <- odb.open(odbFile)
  
  # New tables
  SQL <- c(
    "CREATE TABLE fruits (
      name VARCHAR(6) PRIMARY KEY,
      color VARCHAR(32)
      )",
    "CREATE TABLE vegetables (
      name VARCHAR(6) PRIMARY KEY,
      color VARCHAR(32)
      )"
    )
  odb.write(ODB, SQL)
  
  # Setting a single comment
  odb.comments(ODB,
    tableNames = "fruits",
    columnNames = "name"
  ) <- "Fruit names"
  print(odb.comments(ODB))
  
  # Setting two comments in the same table
  odb.comments(ODB,
    tableNames = "fruits",
    columnNames = c("name", "color")
  ) <- "Fruit columns"
  print(odb.comments(ODB))
  
  # Setting two distinct comments
  odb.comments(ODB,
    tableNames = c("fruits", "vegetables"),
    columnNames = c("name", "color")
  ) <- c("Fruit names", "Vegetable colors")
  print(odb.comments(ODB))
  
  # Writes to the file and closes the connection
  odb.close(ODB, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  ODB <- odb.open(odbFile)
  
  # New tables
  SQL <- c(
    "CREATE TABLE fruits (
      name VARCHAR(6) PRIMARY KEY,
      color VARCHAR(32)
      )",
    "CREATE TABLE vegetables (
      name VARCHAR(6) PRIMARY KEY,
      color VARCHAR(32)
      )"
    )
  odb.write(ODB, SQL)
  
  # Setting a single comment
  odb.comments(ODB,
    tableNames = "fruits",
    columnNames = "name"
  ) <- "Fruit names"
  print(odb.comments(ODB))
  
  # Setting two comments in the same table
  odb.comments(ODB,
    tableNames = "fruits",
    columnNames = c("name", "color")
  ) <- "Fruit columns"
  print(odb.comments(ODB))
  
  # Setting two distinct comments
  odb.comments(ODB,
    tableNames = c("fruits", "vegetables"),
    columnNames = c("name", "color")
  ) <- c("Fruit names", "Vegetable colors")
  print(odb.comments(ODB))
  
  # Writes to the file and closes the connection
  odb.close(ODB, write=TRUE)

Creates a .odb empty file.

Description

Creates an empty HSQL database embedded in a .odb file, copying a template.

Usage

  odb.create(odbFile, template = NULL,
    overwrite = c("warning", "do", "skip", "stop"))
odb.create(odbFile, template = NULL,
    overwrite = c("warning", "do", "skip", "stop"))

Arguments

`odbFile`	Path to the new file.
`template`	Template to copy. You should not have to care about it, as the current version is included in the package (used if NULL).
`overwrite`	Single character value, defining how to handle overwriting : 'warning' will overwrite and raise a warning if a file is replaced, 'stop' will raise an error before copying anything, 'do' will overwrite silently, 'skip' won't silently.

Value

Invisibly returns the single logical value returned by file.copy, if no critical error occurs before it is called.

Note

The default template was produced with LibreOffice Base 3.5.5.

To use a different template once, just use the template argument of this function. Notice a non empty database can be used as template, it will be copied and only the copy will be updated.

To update the default template, replace the "template.odb" file in the "tools" directory of the package with a new one. Usual templates are empty HSQL databases created with OpenOffice or LibreOffice, and saved as .odb files.

Notice that newer templates may require a different version of the hsql.jar library in the odb.open call (an error will be raised if necessary). See odb.open for further details on it.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # Empty template
  print(odb.tables(odb))
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
  
  
  # Use as template
  odbFile2 <- tempfile(fileext=".odb")
  odb.create(odbFile2, template=odbFile, overwrite="do")
  odb <- odb.open(odbFile2)
  print(odb.tables(odb))
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # Empty template
  print(odb.tables(odb))
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
  
  
  # Use as template
  odbFile2 <- tempfile(fileext=".odb")
  odb.create(odbFile2, template=odbFile, overwrite="do")
  odb <- odb.open(odbFile2)
  print(odb.tables(odb))
  odb.close(odb, write=TRUE)

Exports an ODB database to a SQL file.

Description

Produces SQL queries describing the structure of the database and its content, and saves it to a file.

Usage

  odb.export(odb, file)
odb.export(odb, file)

Arguments

`odb`	An `ODB` object, as produced by `odb.open`.
`file`	Path to the file in which export the SQL queries.

Value

Invisibly returns TRUE if succeeds, raises an error if not.

Note

It is just a wrapper for the "SCRIPT '[file]'" SQL query, as implemented in HSQLDB.

Column comments and queries won't be exported, as they are not stored in the HSQL database.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Export to a file
  sqlFile <- tempfile(fileext=".odb")
  odb.export(odb, sqlFile)
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Export to a file
  sqlFile <- tempfile(fileext=".odb")
  odb.export(odb, sqlFile)
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)

Wrapper for inserting data in an ODB table.

Description

Translates a data.frame into "INSERT INTO" SQL queries adaptated to a specific table from the database. Can execute the queries directly if asked to.

Usage

  odb.insert(odb, tableName, data, execute = TRUE,
    dateFormat = "%Y-%m-%d", ...)
odb.insert(odb, tableName, data, execute = TRUE,
    dateFormat = "%Y-%m-%d", ...)

Arguments

`odb`	An `ODB` object, as produced by `odb.open`.
`tableName`	Single character value, naming the table from the database in which insert the data. No quoting is added so the HSQL engine will convert it to upper case, to refer to a case-specific table name you are required to double-quote this value.
`data`	An object coercible to data.frame, containing the data to insert into the database. Column count and order must match those of the database table, R `NA` values will be considered as SQL `NULL` values.
`execute`	Single logical value. If TRUE, the data will be inserted in the database, if FALSE the queries will be returned but not executed.
`dateFormat`	Single character value, defining how dates in "data" are formated. See the "format" argument from `strptime` for more details.
`...`	Further arguments for `odb.write`, if "execute" is set to TRUE.

Value

Returns a multiple character vector, with a distinct SQL query for each row of "data". If "execute" is set to TRUE, the return is invisible.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  
  ## CASE-INSENSITIVE
  
  # New table
  SQL <- "CREATE TABLE fruits (
    name VARCHAR(6) PRIMARY KEY,
    color VARCHAR(32)
  )"
  odb.write(odb, SQL)
  
  # Data insertion
  dat <- data.frame(
    c("banana", "pear", "peach"),
    c("yellow", "yellow", "purple")
  )
  odb.insert(odb, "fruits", dat)
  
  # Check content
  print(odb.read(odb, "SELECT * FROM fruits"))
  
  
  ## CASE-SENSITIVE
  
  # New table
  SQL <- "CREATE TABLE \"Fruits\" (
    name VARCHAR(6) PRIMARY KEY,
    color VARCHAR(32)
  )"
  odb.write(odb, SQL)
  
  # Data insertion
  dat <- data.frame(
    c("banana", "pear", "peach"),
    c("yellow", "yellow", "purple")
  )
  odb.insert(odb, "\"Fruits\"", dat)
  
  # Check content
  print(odb.read(odb, "SELECT * FROM \"Fruits\""))
  
  
  # Notice they are distinct tables
  print(odb.tables(odb))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  
  ## CASE-INSENSITIVE
  
  # New table
  SQL <- "CREATE TABLE fruits (
    name VARCHAR(6) PRIMARY KEY,
    color VARCHAR(32)
  )"
  odb.write(odb, SQL)
  
  # Data insertion
  dat <- data.frame(
    c("banana", "pear", "peach"),
    c("yellow", "yellow", "purple")
  )
  odb.insert(odb, "fruits", dat)
  
  # Check content
  print(odb.read(odb, "SELECT * FROM fruits"))
  
  
  ## CASE-SENSITIVE
  
  # New table
  SQL <- "CREATE TABLE \"Fruits\" (
    name VARCHAR(6) PRIMARY KEY,
    color VARCHAR(32)
  )"
  odb.write(odb, SQL)
  
  # Data insertion
  dat <- data.frame(
    c("banana", "pear", "peach"),
    c("yellow", "yellow", "purple")
  )
  odb.insert(odb, "\"Fruits\"", dat)
  
  # Check content
  print(odb.read(odb, "SELECT * FROM \"Fruits\""))
  
  
  # Notice they are distinct tables
  print(odb.tables(odb))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)

Creates a connection to a .odb file

Description

Extracts embedded HSQLDB files from an .odb archive an sets a DBI connection to it, in order to read or write data from the database.

Usage

  odb.open(odbFile, jarFile = NULL)
odb.open(odbFile, jarFile = NULL)

Arguments

`odbFile`	Path to the .odb file to connect to.
`jarFile`	Path to the .jar library of HSQLDB to use in JDBC. You should not have to care about it, as the current version is included in the package (used if NULL).

Value

An object of class "ODB", which will be used by every other functions of the package.

Note

The default hsql.jar library version is 1.8.0.10.

Alternate versions may be required when using .odb files not produced by odb.create, as they can embed various versions of HSQLDB. Attempting to open an .odb file with the wrong hsql.jar library version will raise an error, it is then up to the user to download the correct hsql.jar file and provide it to odb.open via the jarFile argument.

HyperSQL .jar libraries can be downloaded freely from http://www.hsqldb.org.

The default "hsql.jar" file can be replaced in the "tools" directory of the package if a different version is frequently required.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)

Gets or sets stored queries in an ODB database

Description

This function allows stored SQL queries manipulation into OpenOffice Base databases, through an odb connection.

Usage

  odb.queries(odb, queryNames = NULL)
  odb.queries(odb, queryNames) <- value
odb.queries(odb, queryNames = NULL)
  odb.queries(odb, queryNames) <- value

Arguments

`odb`	An `ODB` object, as produced by `odb.open`.
`queryNames`	Character vector naming queries to get or set.
`value`	Character vector, containing the SQL queries to store.

Value

Returns a named character vector of SQL queries.

Queries and Views

These functions manipulate OpenOffice queries, which are stored in the .odb file and not the database itself. They should not be confused with views, which are SQL features handled by the database engine.

Views are more portable (as they are stored in the database), and can be accessed as virtual tables in SQL queries. To manage them, user is required to use the SQL queries "CREATE VIEW" and "DROP VIEW" (with the odb.write in this package context). More informations on these SQL queries can be found in the HSQL documentation.

Note

The user is required to check and keep its queries up-to-date himself.

Queries can also be manipulated manually from OpenOffice.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Single query
  odb.queries(odb, "banana") = "SELECT * FROM fruits WHERE name='banana'"
  print(odb.read(odb, odb.queries(odb, "banana")))
  
  # Multiple queries
  odb.queries(odb, c("banana","pear")) <- c(
    "SELECT * FROM fruits WHERE name='banana'",
    "SELECT * FROM fruits WHERE name='pear'"
  )
  
  # All queries
  print(odb.queries(odb))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  
  # Single query
  odb.queries(odb, "banana") = "SELECT * FROM fruits WHERE name='banana'"
  print(odb.read(odb, odb.queries(odb, "banana")))
  
  # Multiple queries
  odb.queries(odb, c("banana","pear")) <- c(
    "SELECT * FROM fruits WHERE name='banana'",
    "SELECT * FROM fruits WHERE name='pear'"
  )
  
  # All queries
  print(odb.queries(odb))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)

Executes a reading SQL query in an ODB database (SELECT ...)

Description

Executes an SQL query expecting an output through an "odb" connection.

Usage

  odb.read(odb, sqlQuery, stringsAsFactors = FALSE, check.names = FALSE,
    encode = TRUE, autoLogical = TRUE)
odb.read(odb, sqlQuery, stringsAsFactors = FALSE, check.names = FALSE,
    encode = TRUE, autoLogical = TRUE)

Arguments

`odb`	An `ODB` object, as produced by `odb.open`.
`sqlQuery`	A single character value, containing an unique SQL query to be executed.
`stringsAsFactors`	Single logical value : should character columns in the output be turned to factor columns or not.
`check.names`	Single logical value : should column names in the output be made syntactically valid by `make.names` or not.
`encode`	Single logical value : should character values be translated from UTF-8 charset (native charset for ODB files) to the locale one or not.
`autoLogical`	Single logical value : should logical-like columns be converted to logical or not. Notice this is a workaround, the conversion is not properly done by JDBC and the logical column type is guessed from the values.

Value

Returns a data.frame, whose content depends on the SQL query executed.

Note

To query databases built with OpenOffice or LibreOffice, it may be necessary to quote table and/or column names in sqlQuery, as the default behavior of the HSQL engine is to convert unquoted table and column names to uppercases.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  SQL <- "CREATE TABLE fruits (
    name VARCHAR(6) PRIMARY KEY,
    color VARCHAR(32)
  )"
  odb.write(odb, SQL)
  
  # Data insertion
  dat <- data.frame(
    c("banana", "pear", "peach"),
    c("yellow", "yellow", "purple")
  )
  odb.insert(odb, "fruits", dat)
  
  # Read content
  print(odb.read(odb, "SELECT * FROM fruits"))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  SQL <- "CREATE TABLE fruits (
    name VARCHAR(6) PRIMARY KEY,
    color VARCHAR(32)
  )"
  odb.write(odb, SQL)
  
  # Data insertion
  dat <- data.frame(
    c("banana", "pear", "peach"),
    c("yellow", "yellow", "purple")
  )
  odb.insert(odb, "fruits", dat)
  
  # Read content
  print(odb.read(odb, "SELECT * FROM fruits"))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)

Gets description of every table in an ODB database.

Description

Gets description of every tables in the database through an "odb" connection : table names, column names, column SQL and R types.

Usage

  odb.tables(odb)
odb.tables(odb)

Arguments

odb

An ODB object, as produced by odb.open.

Value

Returns a named list, whith an element for every table in the database. Data.frames are returned by dbColumnInfo, updated with comments returned by odb.comments.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New tables
  SQL <- c(
    "CREATE TABLE fruits (
      name VARCHAR(6) PRIMARY KEY,
      color VARCHAR(32)
      )",
    "CREATE TABLE vegetables (
      name VARCHAR(6) PRIMARY KEY,
      color VARCHAR(32)
      )"
    )
  odb.write(odb, SQL)
  
  # Print tables
  print(odb.tables(odb))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New tables
  SQL <- c(
    "CREATE TABLE fruits (
      name VARCHAR(6) PRIMARY KEY,
      color VARCHAR(32)
      )",
    "CREATE TABLE vegetables (
      name VARCHAR(6) PRIMARY KEY,
      color VARCHAR(32)
      )"
    )
  odb.write(odb, SQL)
  
  # Print tables
  print(odb.tables(odb))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)

Executes writing SQL queries in an ODB database (INSERT ...)

Description

Executes an SQL query expecting no output through an "odb" connection.

Usage

  odb.write(odb, sqlQueries, onError = c("warning", "stop"),
    progress = c("console", "file", "none"))
odb.write(odb, sqlQueries, onError = c("warning", "stop"),
    progress = c("console", "file", "none"))

Arguments

`odb`	An `ODB` object, as produced by `odb.open`.
`sqlQueries`	Single or multiple character vector, with queries to be executed ordered in distinct elements. ";" query separation should not be used.
`onError`	Single character vector, defining how to handle SQL errors (using `warning` or `stop`). If "sqlQueries" contains more than one query, "stop" will prevent remaining queries to be executed, while "warning" won't.
`progress`	Single character vector, the type of progression to print when multiple queries are to be executed (See `progress-class` for further details).

Note

To query databases built with OpenOffice or LibreOffice, it may be necessary to quote table and/or column names in sqlQueries, as the default behavior of the HSQL engine is to convert unquoted table and column names to uppercases.

Author(s)

Sylvain Mareschal

Examples

  # New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  print(odb.tables(odb))
  
  # Manual insert
  odb.write(odb, "INSERT INTO fruits VALUES('apple')")
  print(odb.read(odb, "SELECT * FROM fruits"))
  
  # Remove table
  odb.write(odb, "DROP TABLE fruits")
  print(odb.tables(odb))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)
# New empty .odb file
  odbFile <- tempfile(fileext=".odb")
  odb.create(odbFile, overwrite="do")
  odb <- odb.open(odbFile)
  
  # New table
  odb.write(odb, "CREATE TABLE fruits (name VARCHAR(6) PRIMARY KEY)")
  odb.insert(odb, "fruits", c("banana", "pear", "peach"))
  print(odb.tables(odb))
  
  # Manual insert
  odb.write(odb, "INSERT INTO fruits VALUES('apple')")
  print(odb.read(odb, "SELECT * FROM fruits"))
  
  # Remove table
  odb.write(odb, "DROP TABLE fruits")
  print(odb.tables(odb))
  
  # Writes to the file and closes the connection
  odb.close(odb, write=TRUE)

Classes "progress", "progress.file" and "progress.console"

Description

The two last classes inherit from the first one, and describe textual progression outputs.

Objects from the Class

progress is an abstract class that should not be instantiated.

progress.file and progress.console objects are to be created by the new function, as initialize methods are implemented for each of them.

See the Examples section.

progress.file constructor

Objects can be created by new with the following arguments :

main:: Directly transfered in the appropriate slot
iMax:: Directly transfered in the appropriate slot
iCurrent:: Directly transfered in the appropriate slot
nSteps:: Approximative amount of steps, to pass to pretty

progress.console constructor

Objects can be created by new with the following arguments :

main:: Directly transfered in the appropriate slot
iMax:: Directly transfered in the appropriate slot
iCurrent:: Directly transfered in the appropriate slot

Common slots

main:: Single character value, the title to print at beginning
iMax:: Single integer value, the maximum value for the iteration index
iCurrent:: Single integer value, the current value of the iteration index

progress.console slots

pTimes:: Float vector, proc.time returns used to compute the ETA
eraseLength:: Single integer value, nchar in the previous output

progress.file slots

steps:: Integer vector, iteration indexes for which print an output

Methods

initialize: Constructors of the classes, see previous sections.
set: Updates a progression objects. Takes two arguments : progress (the object to update) and iCurrent, the new value for the iteration index. On each update, a message will be printed according to the class of the updated object.

Author(s)

Sylvain Mareschal

Examples

  # File oriented progression
  testFun = function() {
    obj <- new("progress.file", main="Iterating", iMax=20)
    for(i in 1:20) {
      obj = set(obj, i)
      Sys.sleep(0.1)
    }
  }
  testFun()
 
  # Console oriented progression
  testFun = function() {
    obj <- new("progress.console", main="Iterating", iMax=20)
    for(i in 1:20) {
      obj = set(obj, i)
      Sys.sleep(0.1)
    }
  }
  testFun()
# File oriented progression
  testFun = function() {
    obj <- new("progress.file", main="Iterating", iMax=20)
    for(i in 1:20) {
      obj = set(obj, i)
      Sys.sleep(0.1)
    }
  }
  testFun()
 
  # Console oriented progression
  testFun = function() {
    obj <- new("progress.console", main="Iterating", iMax=20)
    for(i in 1:20) {
      obj = set(obj, i)
      Sys.sleep(0.1)
    }
  }
  testFun()

Package 'ODB'

Help Index

Open Document Databases (.odb) Management

Description

Details

Author(s)

Examples

Formats a time difference in multiple units

Description

Usage

Arguments

Value

Author(s)

Examples

Checks if a DBI connection is closed

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Class "ODB"

Description

Objects from the Class

Slots

Extends

Methods

Note

Author(s)

See Also

Closes an "ODB" connection and updates the .odb file

Description

Usage

Arguments

Value

Note

Author(s)

See Also

Examples

Gets or sets column comments in an ODB database

Description

Usage

Arguments

Details

Value

Note

Author(s)

Examples

Creates a .odb empty file.

Description

Usage

Arguments

Value

Note

Author(s)

Examples

Exports an ODB database to a SQL file.

Description

Usage

Arguments

Value

Note

Author(s)

Examples

Wrapper for inserting data in an ODB table.

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Creates a connection to a .odb file

Description

Usage

Arguments

Value

Note

Author(s)