mdb_env: Create an mdb_env environment

In thor: Interface to 'LMDB'

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

path	The directory in which the database files will reside. If create is TRUE this path will be created for you if it does not exist (in contrast with the lmdb C API). If subdir is FALSE this is the path to the database file and an additional lock file will be created by appending "-lock" to path.
mode	The file mode (UNIX file permissions) to set on created files. this must be an octmode object, with the default (as.octmode("644") being user-writeable and world-readable.
subdir	By default, lmdb creates its files within a directory (at path). If subdir = FALSE then the path is interpreted as the path to the main database file and a lock file will be created with "-lock" appended to the filename. Passing subdir = FALSE is equivalent to lmdb's MDB_NOSUBDIR flag.
readonly	Open the environment in read-only mode. No write operations are allowed. LMDB will still modify the lock file. Passing readonly = TRUE is equivalent to lmdb's MDB_RDONLY flag. If you want a to modify nothing no disk, pass lock = FALSE also (but beware that concurrent access may not go to plan).
metasync	If FALSE, flush system buffers to disk only once per transaction, omit the metadata flush. Defer that until the system flushes files to disk, or next commit or the next call to the $sync() method. This optimization maintains database integrity, but a system crash may undo the last committed transaction. I.e. it preserves the A, C and I (atomicity, consistency, isolation) properties but not D (durability) database property. Passing metasync = FALSE is equivalent to lmdb's MDB_NOMETASYNC flag.
sync	If FALSE, don't flush system buffers to disk when committing a transaction. This optimization means a system crash can corrupt the database or lose the last transactions if buffers are not yet flushed to disk. The risk is governed by how often the system flushes dirty buffers to disk and how often the $sync() method is called. However, if the filesystem preserves write order and writemap = FALSE, transactions exhibit ACI (atomicity, consistency, isolation) properties and only lose D (durability). I.e. database integrity is maintained, but a system crash may undo the final transactions. Note that sync = FALSE, writemap = TRUE leaves the system with no hint for when to write transactions to disk, unless $sync() is called. map_async = TRUE, writemap = TRUE may be preferable. Passing sync = FALSE is equivalent to lmdb's MDB_NOSYNC flag.
writemap	If TRUE, use a writeable memory map unless readonly = TRUE is set. This uses fewer mallocs but loses protection from application bugs like wild pointer writes and other bad updates into the database. This may be slightly faster for databases that fit entirely in RAM, but is slower for databases larger than RAM. Incompatible with nested transactions. Do not mix processes with writemap = TRUE and writemap = FALSE on the same environment. This can defeat durability ($sync() etc). Passing writemap = TRUE is equivalent to lmdb's MDB_WRITEMAP flag.
lock	If FALSE, don't do any locking. If concurrent access is anticipated, the caller must manage all concurrency itself. For proper operation the caller must enforce single-writer semantics, and must ensure that no readers are using old transactions while a writer is active. The simplest approach is to use an exclusive lock so that no readers may be active at all when a writer begins. Passing lock = FALSE is equivalent to lmdb's MDB_NOLOCK flag.
mapasync	If TRUE, When using writemap = TRUE, use asynchronous flushes to disk. As with sync = FALSE, a system crash can then corrupt the database or lose the last transactions. Calling $sync() ensures on-disk database integrity until next commit. Passing mapasync = FALSE is equivalent to lmdb's MDB_MAPASYNC flag.
rdahead	If FALSE, turn off readahead. Most operating systems perform readahead on read requests by default. This option turns it off if the OS supports it. Turning it off may help random read performance when the DB is larger than RAM and system RAM is full. rdahead = FALSE is not implemented on Windows. Passing rdahead = FALSE is equivalent to lmdb's MDB_NORDAHEAD flag.
meminit	If FALSE, don't initialize malloc'd memory before writing to unused spaces in the data file. By default, memory for pages written to the data file is obtained using malloc. While these pages may be reused in subsequent transactions, freshly malloc'd pages will be initialized to zeroes before use. This avoids persisting leftover data from other code (that used the heap and subsequently freed the memory) into the data file. Note that many other system libraries may allocate and free memory from the heap for arbitrary uses. E.g., stdio may use the heap for file I/O buffers. This initialization step has a modest performance cost so some applications may want to disable it using this flag. This option can be a problem for applications which handle sensitive data like passwords, and it makes memory checkers like Valgrind noisy. This flag is not needed with writemap = TRUE, which writes directly to the mmap instead of using malloc for pages. Passing meminit = FALSE is equivalent to lmdb's MDB_NOMEMINIT.
maxdbs	The number of databases available within the environment. If 0 (the default), then the environment holds just one database (the main db). To use named databases this must be set greater than one.
maxreaders	Maximum number of simultaneous read transactions. Can only be set in the first process to open an environment.
mapsize	Maximum size database may grow to; used to size the memory mapping. This is measured in bytes, and the default (as set in lmdb) is only 1MB (2^20 bytes). If database grows larger than map_size, an error will be thrown and the user must close and reopen the mdb_env. On 64-bit there is no penalty for making this huge (say 1TB). Must be <2GB on 32-bit. Increasing this may cause your operating system to report the disk as being used while your database is open, though this is just the amount reserved.
reversekey	Passed through to open_database for the main database. If TRUE, keys are strings to be compared in reverse order, from the end of the strings to the beginning (e.g., DNS names). By default, keys are treated as strings and compared from beginning to end. Passing reversekey = TRUE is equivalent to lmdb's MDB_REVERSEKEY.
create	If FALSE, do not create the directory path if it is missing.

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"))

thor documentation built on Feb. 16, 2023, 9:37 p.m.