Fsdb::Filter::dbjoin

NAME

dbjoin - join two tables on common columns

SYNOPSIS

dbjoin [-Sid] --input table1.fsdb --input table2.fsdb [-nNrR] column [column...]

cat table1.fsdb | dbjoin [-Sid] --input table2.fsdb [-nNrR] column [column...]

DESCRIPTION

Does a natural, inner join on TABLE1 and TABLE2 the specified columns. With the "-a" option, or with "-t outer" it will do a natural, full outer join.

(Database review: inner joints output records only when there are matches in both tables and will omit records that do not match. Outer joins output all records from both tables, filling with the empty value as needed. Right (left) outer joins keep all elements of the right (left) table, even those that don’t match in the other table.)

By default for non-hash joins, data will be sorted lexically, but the usual sorting options can be mixed with the column specification.

Because two tables are required, input is typically in files. Standard input is accessible by the file "-".

If only one input is given, the first (left) input is taken from stdin.

RESOURCE REQUIREMENTS AND PERFORMANCE

Joins can be expensive. Most databases have a query optimizer that knows something about the data and so can select algorithms for efficent operation, in Fsdb, you are that optimizer.

For non-hash joins: If data is already sorted, dbjoin will run more efficiently by telling dbjoin the data is sorted with the "-S".

The resource requirements dbjoin vary. If input data is sorted and "-S" is given, then memory consumption is bounded by the the sum of the largest number of records in either dataset with the same value in the join column, and there is no disk consumption. If data is not sorted, then dbjoin requires disk storage the size of both input files.

One can minimize memory consumption by making sure each record of table1 matches relatively few records in table2. Typically this means that table2 should be the smaller. For example, given two files: people.fsdb (schema: name iso_country_code) and countries.fsdb (schema: iso_country_code full_country_name), then

dbjoin -i people.fsdb -i countries.fsdb iso_country_code

will require less memory than

dbjoin -i countries.fsdb -i people.fsdb iso_country_code

if there are many people per country (as one would expect). If warning "lots of matching rows accumulating in memory" appears, this is the cause and try swapping join order.

For hash joins (that is, with "-m righthash" or "-m lefthash"): all of the right table (the second input) or the left (the first) is loaded into memory (and "hashed"). The other table need not be sorted. Runtime is O(n), but memory is O(size of hashed table).

OPTIONS

-a or --all

Perform a full outer join, include non-matches (each record which doesn’t match at all will appear once). Default is an inner join.

-t TYPE or --type TYPE

Explicitly specify the join type. TYPE must be inner, outer, left (outer), right (outer). (Recall tha inner join requires data on both sides, outer joins keep all records from both sides for outer, or all of the first or second input for left and right outer joins.) Default: inner.

-m METHOD or --method METHOD

Select join method (algorithm). Choices are merge, righthash, and lefthash. Default: merge.

-S or --pre-sorted

assume (and verify) data is already sorted

-e E or --empty E

give value E as the value for empty (null) records

-T TmpDir

where to put tmp files. Also uses environment variable TMPDIR, if -T is not specified. Default is /tmp.

Sort specification options (can be interspersed with column names):
-r or --descending

sort in reverse order (high to low)

-R or --ascending

sort in normal order (low to high)

-n or --numeric

sort numerically

-N or --lexical

sort lexicographically

This module also supports the standard fsdb options:

-d

Enable debugging output.

-i or --input InputSource

Read from InputSource, typically a file name, or "-" for standard input, or (if in Perl) a IO::Handle, Fsdb::IO or Fsdb::BoundedQueue objects.

-o or --output OutputDestination

Write to OutputDestination, typically a file name, or "-" for standard output, or (if in Perl) a IO::Handle, Fsdb::IO or Fsdb::BoundedQueue objects.

--autorun or --noautorun

By default, programs process automatically, but Fsdb::Filter objects in Perl do not run until you invoke the run() method. The "--(no)autorun" option controls that behavior within Perl.

--help

Show help.

--man

Show full manual.

SAMPLE USAGE

Input:
#fsdb sid cid
1 10
2 11
1 12
2 12

And in the file DATA/classes:

#fsdb cid cname
10 pascal
11 numanal
12 os

Command:
cat DATA/reg.fsdb | dbsort -n cid | dbjoin -i - -i DATA/classes -n cid

Output:
#fsdb cid sid cname
10 1 pascal
11 2 numanal
12 1 os
12 2 os
# - COMMENTS:
# | /home/johnh/BIN/DB/dbsort -n cid
# DATA/classes COMMENTS:
# joined comments:
# | /home/johnh/BIN/DB/dbjoin - DATA/classes cid

CLASS FUNCTIONS

new
$filter = new Fsdb::Filter::dbjoin(@arguments);

Create a new dbjoin object, taking command-line arguments.

set_defaults
$filter->set_defaults();

Internal: set up defaults.

parse_options
$filter->parse_options(@ARGV);

Internal: parse command-line arguments.

setup
$filter->setup();

Internal: setup, parse headers.

run_merge_join
$filter->run_merge_join();

Internal: run over each rows.

run_hash_join
$filter->run_hash_join();

Internal: run over each rows, doing a hash join.

run
$filter->run();