Use mdb transactions

Description

Cursors are required for some advanced queries on an mdb database, when the basic set of functions in mdb_txn is not sufficient.

Details

Cursors must be created from within a transaction (which in turn are created from an environment).

Methods

close

Close the cursor

Usage: close()

Value: None, called for side effects only

Note: In lmdb.h this is mdb_cursor_close()

put

Store data using the cursor

Usage: put(key, value, overwrite = TRUE, append = FALSE)

Arguments:

• key: The key (string or raw)

• value: The value (string or raw)

• overwrite: As for mdb_txn $put

• append: As for mdb_txn $put

Value: Logical scalar, indicating if data was previously stored at this key

Note: In lmdb.h this is mdb_cursor_put()

del

Delete the current key

Usage: del()

Value: Logical, indicating if a value was deleted (which will be TRUE if the cursor was valid before this operation). Primarily called for its side effect of deleting the data. After deletion, we call mdb_cursor_get with MDB_GET_CURRENT which will re-validate the cursor.

Note: In lmdb.h this is mdb_cursor_del()

replace

Replace a key's current value with a new value, returning the old value. This is like doing a get() followed by a put within a transaction.

Usage: replace(key, value, as_raw = NULL)

Arguments:

• key: The key to replace

• value: The new value to store

• as_raw: Return the value as raw. With a value of NULL it will return a string if possible (i.e., if there are no null bytes) and a raw vector otherwise. With as_raw = TRUE we always return a raw vector. With as_raw = FALSE we always return a string, or throw an error if this is not possible.

pop

Delete a key's value, returning the value just before it was deleted. This is like doing a get followed by a del within a transaction.

Usage: pop(key, as_raw = NULL)

Arguments:

• key: The key to delete

• as_raw: Return the value as raw. With a value of NULL it will return a string if possible (i.e., if there are no null bytes) and a raw vector otherwise. With as_raw = TRUE we always return a raw vector. With as_raw = FALSE we always return a string, or throw an error if this is not possible.

Value: Depending on as_raw and if there is a value stored, NULL, a character string or a raw vector

first

Move the cursor to the first item in the database

Usage: first()

Value: Invisibly, a logical indicating if the cursor position is valid, but primarily called for side effects

last

Move the cursor to the last item in the database

Usage: last()

Value: Invisibly, a logical indicating if the cursor position is valid, but primarily called for side effects

move_next

Move the cursor to the next item in the database. If called while at the last item in the database, this will invalidate the cursor position.

Usage: move_next()

Value: Invisibly, a logical indicating if the cursor position is valid, but primarily called for side effects

move_prev

Move the cursor to the previous item in the database. If called while at the first item in the database, this will invalidate the cursor position.

Usage: move_prev()

Value: Invisibly, a logical indicating if the cursor position is valid, but primarily called for side effects

move_to

Move the cursor to the item in the database with key key. If key does not exist, this will invalidate the cursor position.

Usage: move_to(key)

Arguments:

• key: Key to move to (string or raw)

Value: Invisibly, a logical indicating if the cursor position is valid, but primarily called for side effects

seek

Move the cursor to the item in the database with key equal to or greater than key. If key does not exist and no key with a key greater than key exists, this will invalidate the cursor position.

Usage: seek(key)

Arguments:

• key: Key to seek (string or raw)

Value: Invisibly, a logical indicating if the cursor position is valid, but primarily called for side effects

get

Move to a key and fetch the value

Usage: get(key, as_proxy = FALSE, as_raw = NULL)

Arguments:

• key: The key to find (string or raw)

• as_proxy: Return as an mdb_proxy object?

• as_raw: Return the value as raw. With a value of NULL it will return a string if possible (i.e., if there are no null bytes) and a raw vector otherwise. With as_raw = TRUE we always return a raw vector. With as_raw = FALSE we always return a string, or throw an error if this is not possible.

Value: Depending on as_raw and if there is a value stored, NULL, a character string or a raw vector

is_valid

Test if cursor is valid (i.e., that it is pointing at data that can be retrieved). Cursors start off invalid until placed (e.g., first, last) and can be invalidated by moving off the beginning or end of the database.

Usage: is_valid()

key

Return the current key

Usage: key(as_proxy = FALSE, as_raw = NULL)

Arguments:

• as_proxy: Return as an mdb_proxy object?

• as_raw: Return the value as raw. With a value of NULL it will return a string if possible (i.e., if there are no null bytes) and a raw vector otherwise. With as_raw = TRUE we always return a raw vector. With as_raw = FALSE we always return a string, or throw an error if this is not possible.

value

Return the current value

Usage: value(as_proxy = FALSE, as_raw = NULL)

Arguments:

• as_proxy: Return as an mdb_proxy object?

• as_raw: Return the value as raw. With a value of NULL it will return a string if possible (i.e., if there are no null bytes) and a raw vector otherwise. With as_raw = TRUE we always return a raw vector. With as_raw = FALSE we always return a string, or throw an error if this is not possible.

Examples

# Start by creating a new environment, and within that a write
# transaction, and from that a new cursor.  But first put a bunch
# of data into the database
env <- thor::mdb_env(tempfile())
env$mput(letters, LETTERS)
txn <- env$begin(write = TRUE)
cur <- txn$cursor()

# Move the cursor to the first position
cur$first()

# The key and value:
cur$key()
cur$value()

# Move to a different key:
cur$move_to("g")
cur$value()

# Delete the current item
cur$del()
cur$key()

# We can't move to 'g' any more as it's gone:
(cur$move_to("g"))
cur$key() # NULL

# But we can *seek* 'g', which will move to 'h'
(cur$seek("g"))
cur$key() # "h"

# Get raw values out:
cur$value(as_raw = TRUE)

# Cleanup
env$destroy()

Use mdb transactions

Description

Database handles are fairly opaque objects used to indicate which database within an mdb_env operations will happen to. This object has therefore got very few methods, all of which are purely informative. Most commonly, a mdb_dbi object will be passed into the mdb_env's $begin() method to begin a transaction on a particular database.

Methods

path

Return the absolute path to the LMDB store (on disk)

Usage: path()

Value: A string

Note: In lmdb.h this is mdb_env_get_path()

flags

Return flags as used in construction of the LMDB environment

Usage: flags()

Value: A named logical vector. Names correspond to arguments to the constructor.

Note: In lmdb.h this is mdb_env_get_flags()

info

Brief information about the LMDB environment

Usage: info()

Value: An integer vector with elements mapsize, last_pgno, last_txnid, maxreaders and numreaders.

Note: In lmdb.h this is mdb_env_info()

stat

Brief statistics about the LMDB environment.

Usage: stat()

Value: An integer vector with elements psize (the size of a database page), depth (depth of the B-tree), brancb_pages (number of internal non-leaf) pages), leaf_pages (number of leaf pages), overflow_pages (number of overflow pages) and entries (number of data items).

Note: In lmdb.h this is mdb_env_stat()

maxkeysize

The maximum size of a key (the value can be bigger than this)

Usage: maxkeysize()

Value: A single integer

Note: In lmdb.h this is mdb_env_get_maxkeysize()

maxreaders

The maximum number of readers

Usage: maxreaders()

Value: A single integer

Note: In lmdb.h this is mdb_env_get_maxreaders()

begin

Begin a transaction

Usage: begin(db = NULL, write = FALSE, sync = NULL, metasync = NULL)

Arguments:

• db: A database handle, as returned by open_database. If NULL (the default) then the default database will be used.

• write: Scalar logical, indicating if this should be a write transaction. There can be only one write transaction per database (see mdb_txn for more details) - it is an error to try to open more than one.

• sync: Scalar logical, indicating if the data should be synchronised synchronised (flushed to disk) after writes; see main parameter list.

• metasync: Scalar logical, indicating if the metadata should be synchronised (flushed to disk) after writes; see main parameter list.

Details: Transactions are the key objects for interacting with an LMDB database (aside from the convenience interface below). They are described in more detail in mdb_txn.

Value: A mdb_txn object

Note: In lmdb.h this is mdb_begin()

with_transaction

Evaluate some code within a transaction

Usage: with_transaction(fun, db = NULL, write = FALSE)

Arguments:

• fun: A function of one argument that does the work of the transaction. with_transaction will pass the transaction to this function. This is most easily explained with an example, so see the bottom of the help

• db: A database handle, as returned by open_database. If NULL (the default) then the default database will be used.

• write: Scalar logical, indicating if this should be a write transaction. There can be only one write transaction per database (see mdb_txn for more details) - it is an error to try to open more than one.

Details: This exists to simplify a pattern where one wants to open a transaction, evaluate some code with that transaction and if anything goes wrong abort, but otherwise commit. It is most useful with read-write transactions, but can be used with both (and the default is for readonly transactions, like begin().

open_database

Open a named database, or return one if already opened.

Usage: open_database(key = NULL, reversekey = FALSE, create = TRUE)

Arguments:

• key: Name of the database; if NULL this returns the default database (always open).

• reversekey: Compare strings in reverse order? See reversekey documentation above

• create: Create database if it does not exist already?

Details: LMDB environments can hold multiple databases, provided they have been opened with maxdbs greater than one. There is always a "default" database - this is unnamed and cannot be dropped. Other databases have a key (i.e., a name) and can be dropped. These database objects are passed through to other methods, notably drop_database and begin

Note: In lmdb.h this is mdb_open()

drop_database

Drop a database

Usage: drop_database(db, delete = TRUE)

Arguments:

• db: A database object, as returned by open_database

• delete: Scalar logical, indicating if the database should be deleted too. If FALSE, the values are deleted from the database (i.e., it is emptied). If TRUE then the actual database is deleted too.

Value: No return value, called for side effects only

Note: In lmdb.h this is mdb_drop()

sync

Flush the data buffers to disk.

Usage: sync(force = FALSE)

Arguments:

• force: Scalar logical; force a synchronous flush. Otherwise if the environment was constructed with sync = FALSE the flushes will be omitted, and with mapasync = TRUE they will be asynchronous.

Details: Data is always written to disk when a transaction is committed, but the operating system may keep it buffered. LMDB always flushes the OS buffers upon commit as well, unless the environment was opened with sync = FALSE or in part metasync = FALSE. This call is not valid if the environment was opened with readonly = TRUE.

Note: In lmdb.h this is mdb_env_sync()

copy

Copy the entire environment state to a new path. This can be used to make a backup of the database.

Usage: copy(path, compact = FALSE)

Arguments:

• path: Scalar character; the new path

• compact: Scalar logical; perform compaction while copying? This omits free pages and sequentially renumbers all pages in output. This can take longer than the default but produce a smaller database

Value: Invisibly, the new path (allowing use of $copy(tempfile))

Note: In lmdb.h this is mdb_env_copy() & mdb_env_copy2()

close

Close the environment. This closes all cursors and transactions (active write transactions are aborted).

Usage: close()

Value: No return value, called for side effects only

Note: In lmdb.h this is mdb_env_close()

destroy

Totally destroy an LMDB environment. This closes the database and removes the files. Use with care!

Usage: destroy()

Value: No return value, called for side effects only

reader_list

List information about database readers

Usage: reader_list()

Value: A character matrix with columns pid (process ID), thread (a pointer address), and txnid (a small integer)

Note: In lmdb.h this is mdb_reader_list()

reader_check

Check for, and remove, stale entries in the reader lock table.

Usage: reader_check()

Value: An integer, being the number of stale readers discarded. However, this function is primarily called for its side effect.

Note: In lmdb.h this is mdb_reader_check()

get

Retrieve a value from the database

Usage: get(key, missing_is_error = TRUE, as_raw = NULL, db = NULL)

Arguments:

• key: A string (or raw vector) - the key to get

• missing_is_error: Logical, indicating if a missing value is an error (by default it is). Alternatively, with missing_is_error = FALSE, a missing value will return NULL. Because no value can be NULL (all values must have nonzero length) a NULL is unambiguously missing.

• as_raw: Either NULL, or a logical, to indicate the result type required. With as_raw = NULL, the default, the value will be returned as a string if possible. If not possible it will return a raw vector. With as_raw = TRUE, get() will always return a raw vector, even when it is possibly to represent the value as a string. If as_raw = FALSE, get will return a string, but throw an error if this is not possible. This is discussed in more detail in the thor vignette (vignette("thor"))

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-only transaction, calls the corresponding method in mdb_txn and then aborts the transaction.

Note: In lmdb.h this is mdb_get()

put

Put values into the database. In other systems, this might be called "set".

Usage: put(key, value, overwrite = TRUE, append = FALSE, db = NULL)

Arguments:

• key: The name of the key (string or raw vector)

• value: The value to save (string or raw vector)

• overwrite: Logical - when TRUE it will overwrite existing data; when FALSE throw an error

• append: Logical - when TRUE, append the given key/value to the end of the database. This option allows fast bulk loading when keys are already known to be in the correct order. But if you load unsorted keys with append = TRUE an error will be thrown

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-write transaction, calls the corresponding method in mdb_txn and then commits the transaction. This will only be possible to use if there is not an existing write transaction in effect for this environment.

Note: In lmdb.h this is mdb_put()

del

Remove a key/value pair from the database

Usage: del(key, db = NULL)

Arguments:

• key: The name of the key (string or raw vector)

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-write transaction, calls the corresponding method in mdb_txn and then commits the transaction. This will only be possible to use if there is not an existing write transaction in effect for this environment.

Value: A scalar logical, indicating if the value was deleted

Note: In lmdb.h this is mdb_del()

exists

Test if a key exists in the database.

Usage: exists(key, db = NULL)

Arguments:

• key: The name of the key to test (string or raw vector). Unlike get, put and del (but like mget, mput and mdel), exists is vectorised. So the input here can be; a character vector of any length (returning the same length logical vector), a raw vector (representing one key, returning a scalar logical) or a list with each element being either a scalar character or a raw vector, returning a logical the same length as the list.

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is an extension of the raw LMDB API and works by using mdb_get for each key (which for lmdb need not copy data) and then testing whether the return value is MDB_SUCCESS or MDB_NOTFOUND.

This is a helper method that establishes a temporary read-only transaction, calls the corresponding method in mdb_txn and then aborts the transaction.

Value: A logical vector

list

List keys in the database

Usage: list(starts_with = NULL, as_raw = FALSE, size = NULL, db = NULL)

Arguments:

• starts_with: Optionally, a prefix for all strings. Note that is not a regular expression or a filename glob. Using foo will match foo, foo:bar and foobar but not fo or FOO. Because LMDB stores keys in a sorted tree, using a prefix can greatly reduce the number of keys that need to be tested.

• as_raw: Same interpretation as as_raw in $get() but with a different default. It is expected that most of the time keys will be strings, so by default we'll try and return a character vector as_raw = FALSE. Change the default if your database contains raw keys.

• size: For use with starts_with, optionally a guess at the number of keys that would be returned. with starts_with = NULL we can look the number of keys up directly so this is ignored.

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-only transaction, calls the corresponding method in mdb_txn and then aborts the transaction.

mget

Get values for multiple keys at once (like $get but vectorised over key)

Usage: mget(key, as_raw = NULL, db = NULL)

Arguments:

• key: The keys to get values for. Zero, one or more keys are allowed.

• as_raw: As for $get(), logical (or NULL) indicating if raw or string output is expected or desired.

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-only transaction, calls the corresponding method in mdb_txn and then aborts the transaction.

mput

Put multiple values into the database (like $put but vectorised over key/value).

Usage: mput(key, value, overwrite = TRUE, append = FALSE, db = NULL)

Arguments:

• key: The keys to set

• value: The values to set against these keys. Must be the same length as key.

• overwrite: As for $put

• append: As for $put

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: The implementation simply calls mdb_put repeatedly (but with a single round of error checking) so duplicate key entries will result in the last key winning.

This is a helper method that establishes a temporary read-write transaction, calls the corresponding method in mdb_txn and then commits the transaction. This will only be possible to use if there is not an existing write transaction in effect for this environment.

mdel

Delete multiple values from the database (like $del but vectorised over key).

Usage: mdel(key, db = NULL)

Arguments:

• key: The keys to delete

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-write transaction, calls the corresponding method in mdb_txn and then commits the transaction. This will only be possible to use if there is not an existing write transaction in effect for this environment.

Value: A logical vector, the same length as key, indicating if each key was deleted.

Examples

# As always, start with the environment.  Because we're going to
# use more than one database, we must set `maxdbs` to more than 1:
env <- thor::mdb_env(tempfile(), maxdbs = 10)

# The default environment - every database
db <- env$open_database()
# The default database will always have id 1 and no name
db$id()
db$name()

# A different database
foo <- env$open_database("foo")
foo$id()
foo$name()

# Opening a database multiple times has no effect - it returns the
# same data base every call.
identical(env$open_database("foo"), foo) # TRUE

# Then we can put some data int the new database:
txn <- env$begin(foo, write = TRUE)
txn$put("hello", "world")
txn$commit()

# Now we have values in the "foo" database, but not the default one:
env$get("hello", db = NULL, missing_is_error = FALSE) # NULL
env$get("hello", db = foo,  missing_is_error = FALSE) # "world"

# Cleanup
env$destroy()

Create an mdb_env environment

Description

Create a mdb_env "environment" object. This is the way that interacts with a lmdb database and once created, includes methods for querying the environment, creating databases, starting transactions and (through those) adding, getting and removing data. This page includes reference documentation for the object and readers are first directed to the vignette (vignette("thor").

Usage

mdb_env(
  path,
  mode = as.octmode("644"),
  subdir = TRUE,
  readonly = FALSE,
  metasync = TRUE,
  sync = TRUE,
  writemap = FALSE,
  lock = TRUE,
  mapasync = FALSE,
  rdahead = TRUE,
  meminit = TRUE,
  maxdbs = NULL,
  maxreaders = NULL,
  mapsize = NULL,
  reversekey = FALSE,
  create = TRUE
)

Arguments

Details

The thor package is a wrapper around lmdb and so below I have provided pointers to relevant options in lmdb - the wrapper is fairly thin and so picks up limitations and restrictions from the underlying library. Some portions of the documentation here derives from the lmdb source documentation - the file lmdb.h in particular.

Methods

path

Return the absolute path to the LMDB store (on disk)

Usage: path()

Value: A string

Note: In lmdb.h this is mdb_env_get_path()

flags

Return flags as used in construction of the LMDB environment

Usage: flags()

Value: A named logical vector. Names correspond to arguments to the constructor.

Note: In lmdb.h this is mdb_env_get_flags()

info

Brief information about the LMDB environment

Usage: info()

Value: An integer vector with elements mapsize, last_pgno, last_txnid, maxreaders and numreaders.

Note: In lmdb.h this is mdb_env_info()

stat

Brief statistics about the LMDB environment.

Usage: stat()

Value: An integer vector with elements psize (the size of a database page), depth (depth of the B-tree), brancb_pages (number of internal non-leaf) pages), leaf_pages (number of leaf pages), overflow_pages (number of overflow pages) and entries (number of data items).

Note: In lmdb.h this is mdb_env_stat()

maxkeysize

The maximum size of a key (the value can be bigger than this)

Usage: maxkeysize()

Value: A single integer

Note: In lmdb.h this is mdb_env_get_maxkeysize()

maxreaders

The maximum number of readers

Usage: maxreaders()

Value: A single integer

Note: In lmdb.h this is mdb_env_get_maxreaders()

begin

Begin a transaction

Usage: begin(db = NULL, write = FALSE, sync = NULL, metasync = NULL)

Arguments:

• db: A database handle, as returned by open_database. If NULL (the default) then the default database will be used.

• write: Scalar logical, indicating if this should be a write transaction. There can be only one write transaction per database (see mdb_txn for more details) - it is an error to try to open more than one.

• sync: Scalar logical, indicating if the data should be synchronised synchronised (flushed to disk) after writes; see main parameter list.

• metasync: Scalar logical, indicating if the metadata should be synchronised (flushed to disk) after writes; see main parameter list.

Details: Transactions are the key objects for interacting with an LMDB database (aside from the convenience interface below). They are described in more detail in mdb_txn.

Value: A mdb_txn object

Note: In lmdb.h this is mdb_begin()

with_transaction

Evaluate some code within a transaction

Usage: with_transaction(fun, db = NULL, write = FALSE)

Arguments:

• fun: A function of one argument that does the work of the transaction. with_transaction will pass the transaction to this function. This is most easily explained with an example, so see the bottom of the help

• db: A database handle, as returned by open_database. If NULL (the default) then the default database will be used.

• write: Scalar logical, indicating if this should be a write transaction. There can be only one write transaction per database (see mdb_txn for more details) - it is an error to try to open more than one.

Details: This exists to simplify a pattern where one wants to open a transaction, evaluate some code with that transaction and if anything goes wrong abort, but otherwise commit. It is most useful with read-write transactions, but can be used with both (and the default is for readonly transactions, like begin().

open_database

Open a named database, or return one if already opened.

Usage: open_database(key = NULL, reversekey = FALSE, create = TRUE)

Arguments:

• key: Name of the database; if NULL this returns the default database (always open).

• reversekey: Compare strings in reverse order? See reversekey documentation above

• create: Create database if it does not exist already?

Details: LMDB environments can hold multiple databases, provided they have been opened with maxdbs greater than one. There is always a "default" database - this is unnamed and cannot be dropped. Other databases have a key (i.e., a name) and can be dropped. These database objects are passed through to other methods, notably drop_database and begin

Note: In lmdb.h this is mdb_open()

drop_database

Drop a database

Usage: drop_database(db, delete = TRUE)

Arguments:

• db: A database object, as returned by open_database

• delete: Scalar logical, indicating if the database should be deleted too. If FALSE, the values are deleted from the database (i.e., it is emptied). If TRUE then the actual database is deleted too.

Value: No return value, called for side effects only

Note: In lmdb.h this is mdb_drop()

sync

Flush the data buffers to disk.

Usage: sync(force = FALSE)

Arguments:

• force: Scalar logical; force a synchronous flush. Otherwise if the environment was constructed with sync = FALSE the flushes will be omitted, and with mapasync = TRUE they will be asynchronous.

Details: Data is always written to disk when a transaction is committed, but the operating system may keep it buffered. LMDB always flushes the OS buffers upon commit as well, unless the environment was opened with sync = FALSE or in part metasync = FALSE. This call is not valid if the environment was opened with readonly = TRUE.

Note: In lmdb.h this is mdb_env_sync()

copy

Copy the entire environment state to a new path. This can be used to make a backup of the database.

Usage: copy(path, compact = FALSE)

Arguments:

• path: Scalar character; the new path

• compact: Scalar logical; perform compaction while copying? This omits free pages and sequentially renumbers all pages in output. This can take longer than the default but produce a smaller database

Value: Invisibly, the new path (allowing use of $copy(tempfile))

Note: In lmdb.h this is mdb_env_copy() & mdb_env_copy2()

close

Close the environment. This closes all cursors and transactions (active write transactions are aborted).

Usage: close()

Value: No return value, called for side effects only

Note: In lmdb.h this is mdb_env_close()

destroy

Totally destroy an LMDB environment. This closes the database and removes the files. Use with care!

Usage: destroy()

Value: No return value, called for side effects only

reader_list

List information about database readers

Usage: reader_list()

Value: A character matrix with columns pid (process ID), thread (a pointer address), and txnid (a small integer)

Note: In lmdb.h this is mdb_reader_list()

reader_check

Check for, and remove, stale entries in the reader lock table.

Usage: reader_check()

Value: An integer, being the number of stale readers discarded. However, this function is primarily called for its side effect.

Note: In lmdb.h this is mdb_reader_check()

get

Retrieve a value from the database

Usage: get(key, missing_is_error = TRUE, as_raw = NULL, db = NULL)

Arguments:

• key: A string (or raw vector) - the key to get

• missing_is_error: Logical, indicating if a missing value is an error (by default it is). Alternatively, with missing_is_error = FALSE, a missing value will return NULL. Because no value can be NULL (all values must have nonzero length) a NULL is unambiguously missing.

• as_raw: Either NULL, or a logical, to indicate the result type required. With as_raw = NULL, the default, the value will be returned as a string if possible. If not possible it will return a raw vector. With as_raw = TRUE, get() will always return a raw vector, even when it is possibly to represent the value as a string. If as_raw = FALSE, get will return a string, but throw an error if this is not possible. This is discussed in more detail in the thor vignette (vignette("thor"))

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-only transaction, calls the corresponding method in mdb_txn and then aborts the transaction.

Note: In lmdb.h this is mdb_get()

put

Put values into the database. In other systems, this might be called "set".

Usage: put(key, value, overwrite = TRUE, append = FALSE, db = NULL)

Arguments:

• key: The name of the key (string or raw vector)

• value: The value to save (string or raw vector)

• overwrite: Logical - when TRUE it will overwrite existing data; when FALSE throw an error

• append: Logical - when TRUE, append the given key/value to the end of the database. This option allows fast bulk loading when keys are already known to be in the correct order. But if you load unsorted keys with append = TRUE an error will be thrown

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-write transaction, calls the corresponding method in mdb_txn and then commits the transaction. This will only be possible to use if there is not an existing write transaction in effect for this environment.

Note: In lmdb.h this is mdb_put()

del

Remove a key/value pair from the database

Usage: del(key, db = NULL)

Arguments:

• key: The name of the key (string or raw vector)

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-write transaction, calls the corresponding method in mdb_txn and then commits the transaction. This will only be possible to use if there is not an existing write transaction in effect for this environment.

Value: A scalar logical, indicating if the value was deleted

Note: In lmdb.h this is mdb_del()

exists

Test if a key exists in the database.

Usage: exists(key, db = NULL)

Arguments:

• key: The name of the key to test (string or raw vector). Unlike get, put and del (but like mget, mput and mdel), exists is vectorised. So the input here can be; a character vector of any length (returning the same length logical vector), a raw vector (representing one key, returning a scalar logical) or a list with each element being either a scalar character or a raw vector, returning a logical the same length as the list.

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is an extension of the raw LMDB API and works by using mdb_get for each key (which for lmdb need not copy data) and then testing whether the return value is MDB_SUCCESS or MDB_NOTFOUND.

This is a helper method that establishes a temporary read-only transaction, calls the corresponding method in mdb_txn and then aborts the transaction.

Value: A logical vector

list

List keys in the database

Usage: list(starts_with = NULL, as_raw = FALSE, size = NULL, db = NULL)

Arguments:

• starts_with: Optionally, a prefix for all strings. Note that is not a regular expression or a filename glob. Using foo will match foo, foo:bar and foobar but not fo or FOO. Because LMDB stores keys in a sorted tree, using a prefix can greatly reduce the number of keys that need to be tested.

• as_raw: Same interpretation as as_raw in $get() but with a different default. It is expected that most of the time keys will be strings, so by default we'll try and return a character vector as_raw = FALSE. Change the default if your database contains raw keys.

• size: For use with starts_with, optionally a guess at the number of keys that would be returned. with starts_with = NULL we can look the number of keys up directly so this is ignored.

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-only transaction, calls the corresponding method in mdb_txn and then aborts the transaction.

mget

Get values for multiple keys at once (like $get but vectorised over key)

Usage: mget(key, as_raw = NULL, db = NULL)

Arguments:

• key: The keys to get values for. Zero, one or more keys are allowed.

• as_raw: As for $get(), logical (or NULL) indicating if raw or string output is expected or desired.

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-only transaction, calls the corresponding method in mdb_txn and then aborts the transaction.

mput

Put multiple values into the database (like $put but vectorised over key/value).

Usage: mput(key, value, overwrite = TRUE, append = FALSE, db = NULL)

Arguments:

• key: The keys to set

• value: The values to set against these keys. Must be the same length as key.

• overwrite: As for $put

• append: As for $put

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: The implementation simply calls mdb_put repeatedly (but with a single round of error checking) so duplicate key entries will result in the last key winning.

This is a helper method that establishes a temporary read-write transaction, calls the corresponding method in mdb_txn and then commits the transaction. This will only be possible to use if there is not an existing write transaction in effect for this environment.

mdel

Delete multiple values from the database (like $del but vectorised over key).

Usage: mdel(key, db = NULL)

Arguments:

• key: The keys to delete

• db: A database handle that would be passed through to create the transaction (see the $begin method).

Details: This is a helper method that establishes a temporary read-write transaction, calls the corresponding method in mdb_txn and then commits the transaction. This will only be possible to use if there is not an existing write transaction in effect for this environment.

Value: A logical vector, the same length as key, indicating if each key was deleted.

Examples

# Create a new environment (just using defaults)
env <- thor::mdb_env(tempfile())

# At its most simple (using temporary transactions)
env$put("a", "hello world")
env$get("a")

# Or create transactions
txn <- env$begin(write = TRUE)
txn$put("b", "another")
txn$put("c", "value")

# Transaction not committed so value not visible outside our transaction
env$get("b", missing_is_error = FALSE)

# After committing, the values are visible for new transactions
txn$commit()
env$get("b", missing_is_error = FALSE)

# A convenience method, 'with_transaction' exists to allow
# transactional workflows with less code repetition.

# This will get the old value of a key 'a', set 'a' to a new value
# and return the old value:
env$with_transaction(function(txn) {
  val <- txn$get("a")
  txn$put("a", "new_value")
  val
}, write = TRUE)

# If an error occurred, the transaction would be aborted.  So far,
# not very interesting!

# More interesting: implementing redis's RPOPLPUSH that takes the
# last value off of the end of one list and pushes it into the
# start of another.
rpoplpush <- function(env, src, dest) {
  f <- function(txn) {
    # Take the value out of the source list and update
    val <- unserialize(txn$get(src, as_raw = TRUE))
    take <- val[[length(val)]]
    txn$put(src, serialize(val[-length(val)], NULL))

    # Put the value onto the destination list
    val <- unserialize(txn$get(dest, as_raw = TRUE))
    txn$put(dest, serialize(c(val, take), NULL))

    # And we'll return the value that was modified
    take
  }
  env$with_transaction(f, write = TRUE)
}

# Set things up - a source list with numbers 1:5 and an empty
# destination list
env$put("src", serialize(1:5, NULL))
env$put("dest", serialize(integer(0), NULL))

# then try it out:
rpoplpush(env, "src", "dest") # 5
rpoplpush(env, "src", "dest") # 4
rpoplpush(env, "src", "dest") # 3

# Here is the state of the two lists
unserialize(env$get("src"))
unserialize(env$get("dest"))

# The above code will fail if one of the lists is available
env$del("dest")
try(rpoplpush(env, "src", "dest"))

# but because it's in a transaction, this failed attempt leaves src
# unchanged
unserialize(env$get("src"))

Proxy values

Description

Proxy object. These exist to try and exploit LMDB's copy-free design. LMDB can pass back a read-only pointer to memory without copying it. So rather than immediately trying to read the whole thing in, this class provides a "proxy" to the data. At the moment they're not terribly useful - all you can do is get the length, and peek at the first bytes! They are used internally in the package to support cursors.

Methods

data

Return the value from a proxy object

Usage: data(as_raw = NULL)

Arguments:

• as_raw: Return the value as a raw vector? This has the same semantics as mdb_env$get - if NULL then the value will be returned as a string as possible, otherwise as a raw vector. If TRUE then the value is always returned as a raw vector, and if FALSE then the value is always returned as a string (or an error is thrown if that is not possible).

Value: A string or raw vector

head

Read the first n bytes from a proxy

Usage: head(n = 6L, as_raw = NULL)

Arguments:

• n: The number of bytes to read. If n is greater than the length of the object the whole object is returned (same behaviour as head

• as_raw: As for $data()

is_raw

Return whether we know a value to be raw or not. This is affected by whether we have successfully turned the value into a string (in which case we can return FALSE) or if any NULL bytes have been detected. The latter condition may be satisfied by reading the first bit of the proxy with $head()

Usage: is_raw()

Value: A logical if we can, otherwise NULL (for symmetry with as_raw)

is_valid

Test if a proxy object is still valid. Once the proxy is invalid, it cannot be read from any more. Proxies are invalidated if their parent transaction is closed, or if any write operations (e.g., put, del) have occurred.

Usage: is_valid()

Value: Scalar logical

size

The size of the data - the number of characters in the string, or number of bytes in the raw vector.

Usage: size()

Value: Scalar integer

Examples

# Start with a write transaction that has written a little data:
env <- thor::mdb_env(tempfile())
txn <- env$begin(write = TRUE)
txn$put("a", "apple")
txn$put("b", "banana")

# We can get a proxy object back by passing as_proxy = TRUE
p <- txn$get("a", as_proxy = TRUE)
p

# Without copying anything we can get the length of the data
p$size() # == nchar("apple")

# And of course we can get the data
p$data()
p$data(as_raw = TRUE)

# Referencing an invalid proxy is an error, but you can use
# "is_valid()" check to see if it is valid
p$is_valid()

txn$put("c", "cabbage")
p$is_valid()
try(p$data())

# It is possible to read the first few bytes; this might be useful
# to determine if (say) a value is a serialised R object:
txn$put("d", serialize(mtcars, NULL))

# The first 6 bytes of a binary serialised rds object is always
#
#   0x58 0x0a 0x00 0x00 0x00 0x02
#
# for XDR serialisation, or
#
#   0x42 0x0a 0x02 0x00 0x00 0x00
#
# for native little-endian serialisation.
#
# So with a little helper function
is_rds <- function(x) {
  h_xdr <- as.raw(c(0x58, 0x0a, 0x00, 0x00, 0x00, 0x02))
  h_bin <- as.raw(c(0x42, 0x0a, 0x02, 0x00, 0x00, 0x00))
  x6 <- head(x, 6L)
  identical(x6, h_xdr) || identical(x6, h_bin)
}

# We can see that the value stored at 'a' is not rds
p1 <- txn$get("a", as_proxy = TRUE)
is_rds(p1$head(6, as_raw = TRUE))

# But the value stored at 'd' is:
p2 <- txn$get("d", as_proxy = TRUE)
is_rds(p2$head(6, as_raw = TRUE))

# Retrieve and unserialise the value:
head(unserialize(p2$data()))

Use mdb transactions

Description

Transactions are required for every mdb operation. Even when using the convenience functions in mdb_env (get, etc), a transaction is created and committed each time. Within a transaction, either everything happens or nothing happens, and everything gets a single consistent view of the database.

Details

There can be many read transactions per environment, but only one write transactions. Because R is single-threaded, that means that you can only simultaneously write from an mdb environment from a single object - any further attempts to open write transactions it would block forever while waiting for a lock that can't be released because there is only one thread!

Methods

id

Return the mdb internal id of the transaction

Usage: id()

Value: An integer

Note: In lmdb.h this is mdb_txn_id()

stat

Brief statistics about the database. This is the same as mdb_env's stat() but applying to the transaction

Usage: stat()

Value: An integer vector with elements psize (the size of a database page), depth (depth of the B-tree), brancb_pages (number of internal non-leaf) pages), leaf_pages (number of leaf pages), overflow_pages (number of overflow pages) and entries (number of data items).

Note: In lmdb.h this is mdb_stat()

commit

Commit all changes made in this transaction to the database, and invalidate the transaction, and any cursors belonging to it (i.e., once committed the transaction cannot be used again)

Usage: commit()

Value: Nothing, called for its side effects only

Note: In lmdb.h this is mdb_txn_commit()

abort

Abandon all changes made in this transaction to the database, and invalidate the transaction, and any cursors belonging to it (i.e., once aborted the transaction cannot be used again). For read-only transactions there is no practical difference between abort and commit, except that using abort allows the transaction to be recycled more efficiently.

Usage: abort(cache = TRUE)

Arguments:

• cache: Logical, indicating if a read-only transaction should be cached for recycling

Value: Nothing, called for its side effects only

Note: In lmdb.h this is mdb_txn_abort()

cursor

Create a mdb_cursor object in this transaction. This can be used for more powerful database interactions.

Usage: cursor()

Value: A mdb_cursor object.

Note: In lmdb.h this is mdb_cursor_open()

get

Retrieve a value from the database

Usage: get(key, missing_is_error = TRUE, as_proxy = FALSE, as_raw = NULL)

Arguments:

• key: A string (or raw vector) - the key to get

• missing_is_error: Logical, indicating if a missing value is an error (by default it is). Alternatively, with missing_is_error = FALSE, a missing value will return NULL. Because no value can be NULL (all values must have nonzero length) a NULL is unambiguously missing.

• as_proxy: Return a "proxy" object, which defers doing a copy into R. See mdb_proxy for more information.

• as_raw: Either NULL, or a logical, to indicate the result type required. With as_raw = NULL, the default, the value will be returned as a string if possible. If not possible it will return a raw vector. With as_raw = TRUE, get() will always return a raw vector, even when it is possibly to represent the value as a string. If as_raw = FALSE, get will return a string, but throw an error if this is not possible. This is discussed in more detail in the thor vignette (vignette("thor"))

Note: In lmdb.h this is mdb_get()

put

Put values into the database. In other systems, this might be called "set".

Usage: put(key, value, overwrite = TRUE, append = FALSE)

Arguments:

• key: The name of the key (string or raw vector)

• value: The value to save (string or raw vector)

• overwrite: Logical - when TRUE it will overwrite existing data; when FALSE throw an error

• append: Logical - when TRUE, append the given key/value to the end of the database. This option allows fast bulk loading when keys are already known to be in the correct order. But if you load unsorted keys with append = TRUE an error will be thrown

Note: In lmdb.h this is mdb_put()

del

Remove a key/value pair from the database

Usage: del(key)

Arguments:

• key: The name of the key (string or raw vector)

Value: A scalar logical, indicating if the value was deleted

Note: In lmdb.h this is mdb_del()

exists

Test if a key exists in the database.

Usage: exists(key)

Arguments:

• key: The name of the key to test (string or raw vector). Unlike get, put and del (but like mget, mput and mdel), exists is vectorised. So the input here can be; a character vector of any length (returning the same length logical vector), a raw vector (representing one key, returning a scalar logical) or a list with each element being either a scalar character or a raw vector, returning a logical the same length as the list.

Details: This is an extension of the raw LMDB API and works by using mdb_get for each key (which for lmdb need not copy data) and then testing whether the return value is MDB_SUCCESS or MDB_NOTFOUND.

Value: A logical vector

list

List keys in the database

Usage: list(starts_with = NULL, as_raw = FALSE, size = NULL)

Arguments:

• starts_with: Optionally, a prefix for all strings. Note that is not a regular expression or a filename glob. Using foo will match foo, foo:bar and foobar but not fo or FOO. Because LMDB stores keys in a sorted tree, using a prefix can greatly reduce the number of keys that need to be tested.

• as_raw: Same interpretation as as_raw in $get() but with a different default. It is expected that most of the time keys will be strings, so by default we'll try and return a character vector as_raw = FALSE. Change the default if your database contains raw keys.

• size: For use with starts_with, optionally a guess at the number of keys that would be returned. with starts_with = NULL we can look the number of keys up directly so this is ignored.

mget

Get values for multiple keys at once (like $get but vectorised over key)

Usage: mget(key, as_proxy = FALSE, as_raw = NULL)

Arguments:

• key: The keys to get values for. Zero, one or more keys are allowed.

• as_proxy: Logical, indicating if a list of mdb_proxy objects should be returned.

• as_raw: As for $get(), logical (or NULL) indicating if raw or string output is expected or desired.

mput

Put multiple values into the database (like $put but vectorised over key/value).

Usage: mput(key, value, overwrite = TRUE, append = FALSE)

Arguments:

• key: The keys to set

• value: The values to set against these keys. Must be the same length as key.

• overwrite: As for $put

• append: As for $put

Details: The implementation simply calls mdb_put repeatedly (but with a single round of error checking) so duplicate key entries will result in the last key winning.

mdel

Delete multiple values from the database (like $del but vectorised over key).

Usage: mdel(key)

Arguments:

• key: The keys to delete

Value: A logical vector, the same length as key, indicating if each key was deleted.

replace

Use a temporary cursor to replace an item; this function will replace the data held at key and return the previous value (or NULL if it doesn't exist). See mdb_cursor for fuller documentation.

Usage: replace(key, value, as_raw = NULL)

Arguments:

• key: The key to replace

• value: The new value value to st key to

• as_raw: For the returned value, how should the data be returned?

Value: As for $get(), a single data item as either a string or raw vector.

pop

Use a temporary cursor to "pop" an item; this function will delete an item but return the value that it had as it deletes it.

Usage: pop(key, as_raw = NULL)

Arguments:

• key: The key to pop

• as_raw: For the returned value, how should the data be returned?

Value: As for $get(), a single data item as either a string or raw vector.

cmp

Compare two keys for ordering

Usage: cmp(a, b)

Arguments:

• a: A key (string or raw); it need not be in the database

• b: A key to compare with b (string or raw)

Value: A scalar integer, being -1 (if a < b), 0 (if a == b) or 1 (if a > b).

Note: In lmdb.h this is mdb_cmp()

Examples

# Start by creating a new environment, and within that a write
# transaction
env <- thor::mdb_env(tempfile())
txn <- env$begin(write = TRUE)

# With this transaction we can write values and see them as set
txn$put("a", "hello")
txn$get("a")

# But because the transaction is not committed, any new
# transaction will not see the values:
env$get("a", missing_is_error = FALSE) # NULL
txn2 <- env$begin()
txn2$get("a", missing_is_error = FALSE) # NULL

# Once we commit a transaction, *new* transactions will see the
# value
txn$commit()
env$get("a") # "hello"
env$begin()$get("a") # "hello"

# But old transactions retain their consistent view of the database
txn2$get("a", missing_is_error = FALSE)

# Cleanup
env$destroy()

Thor driver for storr

Description

Storr driver for thor. This allows thor to be used as a storage backend with the storr package and presents a higher level content addressable key/value store suitable for storing R objects.

Usage

storr_thor(
  env,
  prefix = "",
  hash_algorithm = NULL,
  default_namespace = "objects"
)

driver_thor(env, prefix = "", hash_algorithm = NULL)

Arguments