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|
#!perl
use 5.010;
use strict;
use warnings FATAL => 'all';
use Test::More;
my $rserve_host = $ENV{RSERVE_HOST} || 'localhost';
my $rserve_port = $ENV{RSERVE_PORT} || 6311;
if (IO::Socket::INET->new(PeerAddr => $rserve_host,
PeerPort => $rserve_port)) {
plan tests => 61;
}
else {
plan skip_all => "Cannot connect to Rserve server at localhost:6311";
}
use Test::Fatal;
use Test::MockObject::Extends;
use Statistics::R::IO::Rserve;
use Statistics::R::REXP::Integer;
use lib 't/lib';
use ShortDoubleVector;
use TestCases;
## load the RserveClient macro
my $problemSeed = 1234; # var provided by WWk env
my $Rserve = {host => $rserve_host}; # fake configuration
use File::Spec;
use File::Path;
use Path::Class;
use File::Slurp qw(read_file);
my $PG = Test::MockObject::Extends->new();
## return the last segment of the path
$PG->mock('fileFromPath',
sub {
my ($self, $path) = (shift, shift);
(File::Spec->splitpath($path))[-1];
});
## creates all of the intermediate directories between the tempDirectory
$PG->mock('surePathToTmpFile',
sub {
my ($self, $file) = (shift, shift);
my $file_path = Path::Class::file($file);
my $file_dir = $file_path->dir;
my $tmp_dir = Path::Class::dir(File::Spec->tmpdir);
$file_dir = File::Spec->catdir($tmp_dir, $file_dir) unless
$tmp_dir->subsumes($file_dir);
File::Path::make_path($file_dir);
File::Spec->catdir($file_dir, $file_path->basename)
});
$PG->mock('warning_message',
sub {
state @WARNING_messages;
my ($self, @messages) = @_;
push @WARNING_messages, @messages;
});
open(my $macrofile, 'extras/WebWork/RserveClient.pl') ||
die "Cannot open file: $!";
eval join('', <$macrofile>) ||
die "Evaluating the macro file failed: $@";
sub check_rserve_eval {
my ($rexp, $expected, $message) = @_;
my @expected_value = (ref($expected) eq ref([]) ?
@{$expected} : $expected);
subtest 'rserve eval ' . $message => sub {
plan tests => 2;
## NOTE: I'm switching the order of comparisons to ensure
## ShortDoubleVector's 'eq' overload is used
## test the one-time query
my @result = rserve_query($rexp);
is_deeply(\@expected_value,
\@result,
$message);
## test the persistent connection
@result = rserve_eval($rexp);
is_deeply(\@expected_value,
\@result,
$message)
}
}
## integer vectors
## serialize 1:3, XDR: true
check_rserve_eval(
'1:3',
Statistics::R::REXP::Integer->new([ 1, 2, 3 ])->to_pl,
'int vector no atts');
## serialize a=1L, b=2L, c=3L, XDR: true
check_rserve_eval(
'c(a=1L, b=2L, c=3L)',
Statistics::R::REXP::Integer->new(
elements => [ 1, 2, 3 ],
attributes => {
names => Statistics::R::REXP::Character->new(['a', 'b', 'c'])
})->to_pl,
'int vector names att');
## double vectors
## serialize 1234.56, XDR: true
check_rserve_eval(
'1234.56',
ShortDoubleVector->new([ 1234.56 ])->to_pl,
'double vector no atts');
## serialize foo=1234.56, XDR: true
check_rserve_eval(
'c(foo=1234.56)',
ShortDoubleVector->new(
elements => [ 1234.56 ],
attributes => {
names => Statistics::R::REXP::Character->new(['foo'])
})->to_pl,
'double vector names att');
## character vectors
## serialize letters[1:3], XDR: true
check_rserve_eval(
'letters[1:3]',
Statistics::R::REXP::Character->new([ 'a', 'b', 'c' ])->to_pl,
'character vector no atts');
## serialize A='a', B='b', C='c', XDR: true
check_rserve_eval(
'c(A="a", B="b", C="c")',
Statistics::R::REXP::Character->new(
elements => [ 'a', 'b', 'c' ],
attributes => {
names => Statistics::R::REXP::Character->new(['A', 'B', 'C'])
})->to_pl,
'character vector names att - xdr');
## raw vectors
## serialize as.raw(c(1:3, 255, 0), XDR: true
check_rserve_eval(
'as.raw(c(1,2,3,255, 0))',
Statistics::R::REXP::Raw->new([ 1, 2, 3, 255, 0 ])->to_pl,
'raw vector');
## list (i.e., generic vector)
## serialize list(1:3, list('a', 'b', 11), 'foo'), XDR: true
check_rserve_eval(
"list(1:3, list('a', 'b', 11), 'foo')",
Statistics::R::REXP::List->new([
Statistics::R::REXP::Integer->new([ 1, 2, 3]),
Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new(['a']),
Statistics::R::REXP::Character->new(['b']),
ShortDoubleVector->new([11]) ]),
Statistics::R::REXP::Character->new(['foo']) ])->to_pl,
'generic vector no atts');
## serialize list(foo=1:3, list('a', 'b', 11), bar='foo'), XDR: true
check_rserve_eval(
"list(foo=1:3, list('a', 'b', 11), bar='foo')",
Statistics::R::REXP::List->new(
elements => [
Statistics::R::REXP::Integer->new([ 1, 2, 3]),
Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new(['a']),
Statistics::R::REXP::Character->new(['b']),
ShortDoubleVector->new([11]) ]),
Statistics::R::REXP::Character->new(['foo']) ],
attributes => {
names => Statistics::R::REXP::Character->new(['foo', '', 'bar'])
})->to_pl,
'generic vector names att - xdr');
## matrix
## serialize matrix(-1:4, 2, 3), XDR: true
check_rserve_eval(
'matrix(-1:4, 2, 3)',
Statistics::R::REXP::Integer->new(
elements => [ -1, 0, 1, 2, 3, 4 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([2, 3]),
})->to_pl,
'int matrix no atts');
## serialize matrix(-1:4, 2, 3, dimnames=list(c('a', 'b'))), XDR: true
check_rserve_eval(
"matrix(-1:4, 2, 3, dimnames=list(c('a', 'b')))",
Statistics::R::REXP::Integer->new(
elements => [ -1, 0, 1, 2, 3, 4 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([2, 3]),
dimnames => Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new(['a', 'b']),
Statistics::R::REXP::Null->new
]),
})->to_pl,
'int matrix rownames');
## data frames
## serialize head(cars)
check_rserve_eval(
'head(cars)',
Statistics::R::REXP::List->new(
elements => [
ShortDoubleVector->new([ 4, 4, 7, 7, 8, 9]),
ShortDoubleVector->new([ 2, 10, 4, 22, 16, 10]),
],
attributes => {
names => Statistics::R::REXP::Character->new(['speed', 'dist']),
class => Statistics::R::REXP::Character->new(['data.frame']),
'row.names' => Statistics::R::REXP::Integer->new([
1, 2, 3, 4, 5, 6
]),
})->to_pl,
'the cars data frame');
## serialize head(mtcars)
check_rserve_eval(
'head(mtcars)',
Statistics::R::REXP::List->new(
elements => [
ShortDoubleVector->new([ 21.0, 21.0, 22.8, 21.4, 18.7, 18.1 ]),
ShortDoubleVector->new([ 6, 6, 4, 6, 8, 6 ]),
ShortDoubleVector->new([ 160, 160, 108, 258, 360, 225 ]),
ShortDoubleVector->new([ 110, 110, 93, 110, 175, 105 ]),
ShortDoubleVector->new([ 3.90, 3.90, 3.85, 3.08, 3.15, 2.76 ]),
ShortDoubleVector->new([ 2.620, 2.875, 2.320, 3.215, 3.440, 3.460 ]),
ShortDoubleVector->new([ 16.46, 17.02, 18.61, 19.44, 17.02, 20.22 ]),
ShortDoubleVector->new([ 0, 0, 1, 1, 0, 1 ]),
ShortDoubleVector->new([ 1, 1, 1, 0, 0, 0 ]),
ShortDoubleVector->new([ 4, 4, 4, 3, 3, 3 ]),
ShortDoubleVector->new([ 4, 4, 1, 1, 2, 1 ]),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'mpg' , 'cyl', 'disp', 'hp', 'drat', 'wt', 'qsec',
'vs', 'am', 'gear', 'carb']),
class => Statistics::R::REXP::Character->new(['data.frame']),
'row.names' => Statistics::R::REXP::Character->new([
'Mazda RX4', 'Mazda RX4 Wag', 'Datsun 710',
'Hornet 4 Drive', 'Hornet Sportabout', 'Valiant'
]),
})->to_pl,
'the mtcars data frame');
## serialize head(iris)
check_rserve_eval(
'head(iris)',
Statistics::R::REXP::List->new(
elements => [
ShortDoubleVector->new([ 5.1, 4.9, 4.7, 4.6, 5.0, 5.4 ]),
ShortDoubleVector->new([ 3.5, 3.0, 3.2, 3.1, 3.6, 3.9 ]),
ShortDoubleVector->new([ 1.4, 1.4, 1.3, 1.5, 1.4, 1.7 ]),
ShortDoubleVector->new([ 0.2, 0.2, 0.2, 0.2, 0.2, 0.4 ]),
Statistics::R::REXP::Integer->new(
elements => [ 1, 1, 1, 1, 1, 1 ],
attributes => {
levels => Statistics::R::REXP::Character->new([
'setosa', 'versicolor', 'virginica']),
class => Statistics::R::REXP::Character->new(['factor'])
} ),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'Sepal.Length', 'Sepal.Width', 'Petal.Length',
'Petal.Width', 'Species']),
class => Statistics::R::REXP::Character->new(['data.frame']),
'row.names' => Statistics::R::REXP::Integer->new([
1, 2, 3, 4, 5, 6
]),
})->to_pl,
'the iris data frame');
## Call lm(mpg ~ wt, data = head(mtcars))
check_rserve_eval(
'lm(mpg ~ wt, data = head(mtcars))$call',
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('lm'),
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('~'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('head'),
Statistics::R::REXP::Symbol->new('mtcars'),
]),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'', 'formula', 'data' ])
})->to_pl,
'language lm(mpg~wt, head(mtcars))');
## serialize lm(mpg ~ wt, data = head(mtcars))
check_rserve_eval(
'lm(mpg ~ wt, data = head(mtcars))',
Statistics::R::REXP::List->new(
elements => [
# coefficients
ShortDoubleVector->new(
elements => [ 30.3002034730204, -3.27948805566774 ],
attributes => {
names => Statistics::R::REXP::Character->new(['(Intercept)', 'wt'])
}),
# residuals
ShortDoubleVector->new(
elements => [ -0.707944767170941, 0.128324687024322, 0.108208816128727,
1.64335062595135, -0.318764561523408, -0.853174800410051 ],
attributes => {
names => Statistics::R::REXP::Character->new([
"Mazda RX4", "Mazda RX4 Wag",
"Datsun 710", "Hornet 4 Drive",
"Hornet Sportabout", "Valiant" ])
}),
# effects
ShortDoubleVector->new(
elements => [ -50.2145397270552, -3.39713386075597, 0.13375416348722,
1.95527848390874, 0.0651588996571721, -0.462851730054076 ],
attributes => {
names => Statistics::R::REXP::Character->new([
'(Intercept)', 'wt', '',
'', '', '' ])
}),
# rank
Statistics::R::REXP::Integer->new([2]),
# fitted.values
ShortDoubleVector->new(
elements => [ 21.7079447671709, 20.8716753129757, 22.6917911838713,
19.7566493740486, 19.0187645615234, 18.9531748004101 ],
attributes => {
names => Statistics::R::REXP::Character->new([
"Mazda RX4", "Mazda RX4 Wag",
"Datsun 710", "Hornet 4 Drive",
"Hornet Sportabout", "Valiant" ])
}),
# assign
Statistics::R::REXP::Integer->new([0, 1]),
# qr
Statistics::R::REXP::List->new(
elements => [
# qr
ShortDoubleVector->new(
elements => [ -2.44948974278318, 0.408248290463863,
0.408248290463863, 0.408248290463863,
0.408248290463863, 0.408248290463863,
-7.31989184801706, 1.03587322261623,
0.542107126002057, -0.321898217952644,
-0.539106265315558, -0.558413647303373 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([ 6, 2 ]),
dimnames => Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new([
"Mazda RX4", "Mazda RX4 Wag",
"Datsun 710", "Hornet 4 Drive",
"Hornet Sportabout", "Valiant" ]),
Statistics::R::REXP::Character->new([
'(Intercept)', 'wt' ])
]),
assign => Statistics::R::REXP::Integer->new([
0, 1
]),
}),
# qraux
ShortDoubleVector->new(
[ 1.40824829046386, 1.0063272758402 ]),
# pivot
Statistics::R::REXP::Integer->new([1, 2]),
# tol
ShortDoubleVector->new([1E-7]),
# rank
Statistics::R::REXP::Integer->new([2]),
],
attributes => {
names => Statistics::R::REXP::Character->new([
"qr", "qraux", "pivot",
"tol", "rank" ]),
class => Statistics::R::REXP::Character->new(['qr'])
}),
# df.residual
Statistics::R::REXP::Integer->new([4]),
# xlevels
Statistics::R::REXP::List->new(
elements => [],
attributes => {
names => Statistics::R::REXP::Character->new([])
}),
# call
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('lm'),
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('~'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('head'),
Statistics::R::REXP::Symbol->new('mtcars'),
]),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'', 'formula', 'data' ])
}),
# terms
Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('~'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
],
attributes => {
variables => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('list'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
factors => Statistics::R::REXP::Integer->new(
elements => [ 0, 1 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([ 2, 1 ]),
dimnames => Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new([
'mpg', 'wt' ]),
Statistics::R::REXP::Character->new([ 'wt' ]),
]),
}),
'term.labels' => Statistics::R::REXP::Character->new(['wt']),
order => Statistics::R::REXP::Integer->new([1]),
intercept => Statistics::R::REXP::Integer->new([1]),
response => Statistics::R::REXP::Integer->new([1]),
class => Statistics::R::REXP::Character->new([
'terms', 'formula'
]),
'.Environment' => Statistics::R::REXP::Unknown->new(sexptype => 4),
predvars => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('list'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
dataClasses => Statistics::R::REXP::Character->new(
elements => ['numeric', 'numeric'],
attributes => {
names => Statistics::R::REXP::Character->new(['mpg', 'wt'])
}),
}),
# model
Statistics::R::REXP::List->new(
elements => [
ShortDoubleVector->new([ 21.0, 21.0, 22.8, 21.4, 18.7, 18.1 ]),
ShortDoubleVector->new([ 2.62, 2.875, 2.32, 3.215, 3.44, 3.46 ]),
],
attributes => {
names => Statistics::R::REXP::Character->new(['mpg', 'wt']),
'row.names' => Statistics::R::REXP::Character->new([
'Mazda RX4', 'Mazda RX4 Wag', 'Datsun 710',
'Hornet 4 Drive', 'Hornet Sportabout', 'Valiant']),
class => Statistics::R::REXP::Character->new(['data.frame']),
terms => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('~'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
],
attributes => {
variables => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('list'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
factors => Statistics::R::REXP::Integer->new(
elements => [ 0, 1 ],
attributes => {
dim => Statistics::R::REXP::Integer->new([ 2, 1 ]),
dimnames => Statistics::R::REXP::List->new([
Statistics::R::REXP::Character->new([
'mpg', 'wt' ]),
Statistics::R::REXP::Character->new([ 'wt' ]),
]),
}),
'term.labels' => Statistics::R::REXP::Character->new(['wt']),
order => Statistics::R::REXP::Integer->new([1]),
intercept => Statistics::R::REXP::Integer->new([1]),
response => Statistics::R::REXP::Integer->new([1]),
class => Statistics::R::REXP::Character->new([
'terms', 'formula'
]),
'.Environment' => Statistics::R::REXP::Unknown->new(sexptype => 4),
predvars => Statistics::R::REXP::Language->new(
elements => [
Statistics::R::REXP::Symbol->new('list'),
Statistics::R::REXP::Symbol->new('mpg'),
Statistics::R::REXP::Symbol->new('wt'),
]),
dataClasses => Statistics::R::REXP::Character->new(
elements => ['numeric', 'numeric'],
attributes => {
names => Statistics::R::REXP::Character->new(['mpg', 'wt'])
}),
}),
}),
],
attributes => {
names => Statistics::R::REXP::Character->new([
'coefficients', 'residuals', 'effects', 'rank',
'fitted.values', 'assign', 'qr', 'df.residual',
'xlevels', 'call', 'terms', 'model',
]),
class => Statistics::R::REXP::Character->new(['lm']) })->to_pl,
'lm mpg~wt, head(mtcars)');
while ( my ($name, $value) = each %{TEST_CASES()} ) {
SKIP: {
skip "not applicable in WebWork macros", 1 if ($value->{skip} || '' =~ 'webwork');
## If the expected value is wrapped in 'RexpOrUnknown', it will
## be XT_UNKNOWN over Rserve
my $expected = $value->{value}->isa('RexpOrUnknown') ?
undef : $value->{value}->to_pl;
check_rserve_eval($value->{expr},
$expected,
$value->{desc});
}
}
subtest 'R runtime errors' => sub {
plan tests => 2;
like(exception {
rserve_eval('1+"a"')
}, qr/Error in 1 \+ "a" : non-numeric argument to binary operator/,
'rserve_eval');
like(exception {
rserve_query('1+"a"')
}, qr/Error in 1 \+ "a" : non-numeric argument to binary operator/,
'rserve_query');
};
subtest 'Rserve plot' => sub {
plan tests => 4;
my $remote = rserve_start_plot();
rserve_eval('plot(1)');
my $local = rserve_finish_plot($remote);
my $png_contents = read_file($local);
ok(-e $local, 'plot file');
ok($png_contents =~ qr/^.PNG\r\n.*IHDR\0\0\x01\xE0\0\0\x01\xE0/s,
'default figure dimensions (480x480)') or
diag('True file type: ' . `file $local`);
Path::Class::file($local)->remove;
$remote = rserve_start_plot('png', 800, 732);
rserve_eval('plot(1)');
$local = rserve_finish_plot($remote);
$png_contents = read_file($local);
ok(-e $local, 'plot file');
ok($png_contents =~ qr/^.PNG\r\n.*IHDR\0\0\x03\x20\0\0\x02\xDC/s,
'custom figure dimensions') or
diag('True file type: ' . `file $local`);
Path::Class::file($local)->remove;
};
my $remote = (rserve_eval("file.path(system.file(package='base'), 'DESCRIPTION')"))[0];
my $local = rserve_get_file($remote);
ok(-e $local, 'rserve remote file');
Path::Class::file($local)->remove;
subtest 'missing configuration' => sub {
plan tests => 2;
undef $Rserve;
$PG->clear;
rserve_query('pi');
my ($request, $args) = $PG->next_call();
is($request,
'warning_message', 'call warning message');
like($args->[1], qr/Calling testing::function is disabled unless Rserve host is configured/,
'missing configuration message')
};
## mock for the Value::traceback function
package Value;
sub traceback {
return " in testing::function at line 123 of some_file"
}
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