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add HTML::TableParser, may change to something else if there is enoug…
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…h complaining
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Chris Fields committed Dec 15, 2011
1 parent 9fc9df5 commit 719cc0d
Showing 1 changed file with 61 additions and 58 deletions.
119 changes: 61 additions & 58 deletions Build.PL
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Expand Up @@ -43,129 +43,132 @@ WARN
}

}

my %recommends = (
# AcePerl support is deprecated, per LDS - cjfields - 5-5-2011

#'Ace' => [0,
# 'Access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace'],

'Algorithm::Munkres' => [0,
'Phylogenetic Networks/Bio::PhyloNetwork'],

'Array::Compare' => [0,
'Phylogenetic Networks/Bio::PhyloNetwork'],

'YAML' => [0,
'GenBank->GFF3/bp_genbank2gff3.pl'],

# this won't actually install due to circular dep, but we have no way of
# doing a post-install the [circular dependency!] specifies it is only
# installed on explicit request for this specific module, not when simply
# choosing to install 'all' modules

#'Bio::ASN1::EntrezGene' => [0,
# 'Parsing entrezgene/Bio::SeqIO::entrezgene [circular dependency!]'],

'Clone' => [0,
'Cloning objects/Bio::Tools::Primer3'],

'Convert::Binary::C' => [0,
'Strider functionality/Bio::SeqIO::strider'],

'Error' => [0,
'OO-based exception handling (very optional)/Bio::Root::Exception'],

'GD' => [0,
'Alignment graphic output/Bio::Align::Graphics'],

'Graph' => [0,
'Phylogenetic Networks, ontology engine implementation, contig analysis'.
'/Bio::PhyloNetwork,Bio::Ontology::SimpleGOEngine::GraphAdaptor,'.
'Bio::Assembly::Tools::ContigSpectrum'],

'GraphViz' => [0,
'Phylogenetic Network Visulization/Bio::PhyloNetwork::GraphViz'],

'HTML::Entities' => [0,
'Remote analysis POST submissions/Bio::SearchIO::blastxml'],

'HTML::HeadParser' => [3,
'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'],


'HTML::TableParser' => [3,
'Parsing HTML tables/Bio::DB::SeqVersion::gi'],

'HTTP::Request::Common' => [0,
'GenBank+GenPept sequence retrieval, remote http Blast jobs'.
'/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'.
'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'],

'List::MoreUtils' => [0,
'Back- or reverse-translation of sequences/'.
'Bio::Tools::SeqPattern,Bio::Tools::SeqPattern::BackTranslate'],

'LWP::UserAgent' => [0,
'Remote access/Bio::DB::*,Bio::Tools::Run::RemoteBlast,Bio::WebAgent'],

'Math::Random' => [0,
'Random Phylogenetic Networks/Bio::PhyloNetwork::RandomFactory'],

'PostScript::TextBlock' => [0,
'EPS output/Bio::Tree::Draw::Cladogram'],

'Set::Scalar' => [0,
'Proper operation/Bio::Tree::Compatible'],

'SOAP::Lite' => [0,
'Bibliographic queries/Bio::DB::Biblio::soap'],

'Sort::Naturally' => [0,
'Sort lexically, but sort numeral parts numerically/'.
'Bio::Assembly::IO::ace,Bio::Assembly::IO::tigr'],

'Spreadsheet::ParseExcel' => [0,
'Parsing Excel files/Bio::SeqIO::excel'],

'Storable' => [2.05,
'Storing sequence objects in local file cache/'.
'Bio::DB::FileCache,Bio::SeqFeature::Collection,Bio::PopGen::HtSNP,'.
'Bio::PopGen::TagHaplotype,Bio::DB::GFF::Adaptor::berkeleydb'],

'SVG' => [2.26,
'Creating SVG images/Bio::Draw::Pictogram'],

'SVG::Graph' => [0.01,
'Creating SVG images/Bio::TreeIO::svggraph'],

'Text::ParseWords' => [0,
'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader'],

'URI::Escape' => [0,
'Dealing with web resources/Bio::FeatureIO::gff,Bio::FeatureIO::interpro,'.
'Bio::DB::Biblio::eutils,Bio::DB::EUtilParameters,'.
'Bio::DB::Query::GenBank,Bio::DB::NCBIHelper,Bio::SeqFeature::Annotated'],

'XML::DOM::XPath' => [0.13,
'parsing interpro features/Bio::FeatureIO::interpro'],

'XML::Parser' => [0,
'parsing xml/Bio::Biblio::IO::medlinexml'],

'XML::Parser::PerlSAX' => [0,
'Parsing XML/Bio::SeqIO::tinyseq,Bio::SeqIO::game::gameSubs,',
'Bio::OntologyIO::InterProParser,Bio::ClusterIO::dbsnp'],

'XML::SAX' => [0.15,
'Parsing XML/Bio::SearchIO::blastxml,Bio::SeqIO::tigrxml,Bio::SeqIO::bsml_sax'],

'XML::SAX::Writer' => [0,
'Writing XML/Bio::SeqIO::tigrxml'],

'XML::Simple' => [0,
'Reading custom XML/Bio::Tools::EUtilities,Bio::DB::HIV,Bio::DB::Query::HIVQuery'],

'XML::Twig' => [0,
'Parsing XML/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,'.
'Bio::DB::Biblio::eutils'],

'XML::Writer' => [0.4,
'Parsing and writing XML/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,'.
'Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,'.
Expand Down Expand Up @@ -193,57 +196,57 @@ my $build = Bio::Root::Build->new(
'Scalar::Util' => 0, # not in Perl 5.6.1, arrived in core in 5.7.3
'ExtUtils::Manifest' => '1.52', # allows spaces in file names
},

build_requires => {
'Test::Most' => 0,
'Module::Build' => 0.2805,
'Test::Harness' => 2.62,
'CPAN' => 1.81
},

recommends => {
# reverted to a simple Module::Build-compatible hash, but we keep
# additional data in the %recommends hash above. May be converted to
# something simpler if there aren't complaints down the line.
map {$_ => $recommends{$_}[0]} sort keys %recommends
},

get_options => {
accept => { },
network => { } # say 'perl Build.PL --network' to manually request network tests
},

auto_features => {
'EntrezGene' => {
description => "Presence of Bio::ASN1::EntrezGene",
requires => { 'Bio::ASN1::EntrezGene' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
},

'DB_File Tests' => {
description => "BDB tests for Bio::DB::SeqFeature::Store",
requires => { 'DB_File' => 0 } # feature_requires is like requires, except that it doesn't trigger installation
},

'Bio::DB::GFF Tests' => {
description => "Bio::DB::GFF database tests (will need to answer questions before really enabling)",
requires => { 'DBI' => 0 },
},

'MySQL Tests' => {
description => "MySQL-related tests for Bio::DB::SeqFeature::Store",
requires => { 'DBI' => 0, 'DBD::mysql' => 0 },
},

'Pg Tests' => {
description => "PostgreSQL-related tests for Bio::DB::SeqFeature::Store",
requires => { 'DBI' => 0, 'DBD::Pg' => 0},
},

'SQLite Tests' => {
description => "SQLite-related tests for Bio::DB::SeqFeature::Store",
requires => { 'DBI' => 0, 'DBD::SQLite' => 0},
},

'Network Tests' => {
description => "Enable tests that need an internet connection",
requires => { 'LWP::UserAgent' => 0 },
Expand All @@ -252,10 +255,10 @@ my $build = Bio::Root::Build->new(
dynamic_config => 1,
#create_makefile_pl => 'passthrough',
recursive_test_files => 1,

# Extra files needed for BioPerl modules
xml_files => {'./Bio/DB/HIV/lanl-schema.xml' => 'lib/Bio/DB/HIV/lanl-schema.xml'},

#pm_files => {} # modules in Bio are treated as if they were in lib and auto-installed
#script_files => [] # scripts in scripts directory are installed on-demand
);
Expand All @@ -272,7 +275,7 @@ however, because it has a circular dependency with BioPerl we do not
include it on our list of recommended modules.
If you require EntrezGene functionality, you can install
Bio::ASN1::EntrezGene after BioPerl has finished installing.
Bio::ASN1::EntrezGene after BioPerl has finished installing.
############################# WARNING #############################
Expand Down Expand Up @@ -324,7 +327,7 @@ exit;
sub make_bdb_test {
my $path0 = File::Spec->catfile('t', 'LocalDB', 'SeqFeature.t');
my $path = File::Spec->catfile('t', 'LocalDB','SeqFeature_BDB.t');
unlink($path) if (-e $path);
unlink($path) if (-e $path);
open(my $F, ">", $path) || die "Can't create test file\n";
print $F <<END;
system '$^X $path0 -adaptor berkeleydb -create 1 -temp 1';
Expand Down Expand Up @@ -385,7 +388,7 @@ sub prompt_for_biodb {
my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ".
"Bio::DB::SeqFeature::Store live database tests? ".
"y/n", 'n');

if ($proceed) {
my @driver_choices;
foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') {
Expand All @@ -395,7 +398,7 @@ sub prompt_for_biodb {
push(@driver_choices, $choice);
}
}

my $driver;
if (@driver_choices > 1) {
my ($default) = $driver_choices[0] =~ /\[(.)/;
Expand All @@ -416,19 +419,19 @@ sub prompt_for_biodb {
elsif ($driver =~ /^[sS]/) {
$driver = 'SQLite';
}

my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n".
"This database should already be present but doesn't have to ".
"be preloaded for any schema", 'test');
my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost');
my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef');
my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef');

my $use_host = 1;
if ($test_host eq 'undef' || $test_host eq 'localhost') {
$use_host = 0;
}

my $test_dsn;
if ($driver eq 'Pg' || $driver eq 'SQLite') {
$test_dsn = "dbi:$driver:dbname=$test_db";
Expand All @@ -441,14 +444,14 @@ sub prompt_for_biodb {
if ($use_host) {
$test_dsn .= ";host=$test_host";
}

$build->notes(dbd_driver => $driver);
$build->notes(test_db => $test_db);
$build->notes(test_host => $test_host);
$build->notes(test_user => $test_user eq 'undef' ? undef : $test_user);
$build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass);
$build->notes(test_dsn => $test_dsn);

$build->log_info(" - will run tests with database driver '$driver' and these settings:\n",
" Database $test_db\n",
" Host $test_host\n",
Expand All @@ -461,7 +464,7 @@ sub prompt_for_biodb {
else {
$build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n");
}

$build->log_info("\n");
return $proceed;
}

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