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sync with trunk

svn path=/bioperl-run/branches/branch-1-6/; revision=15521
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commit e1584edd55ba93a38cdf9603f098bf7f835683fd 1 parent 370dacc
cjfields authored
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15 Bio/Tools/Run/Ensembl.pm
@@ -327,16 +327,15 @@ sub get_gene_by_name {
-term => $taxid ? "$gene_name ${taxid}[taxid]" : "$gene_name \"$species\"[Organism]",
-usehistory => 'y',
-verbose => -1);
- $esearch->get_response;
my $esummary = Bio::DB::EUtilities->new(-eutil => 'esummary',
- -cookie => $esearch->next_cookie);
- eval {$esummary->get_response;};
- unless ($@) {
+ -history => $esearch->next_History);
+ eval {$esummary->parse_data;};
+ if (!$@) {
my $ncbi_id;
- foreach my $docsum ($esummary->get_all_docsums) {
- my %item = $docsum->get_item_by_name('Name');
- if (lc($item{Content}) eq lc($gene_name)) {
- $ncbi_id = $docsum->esummary_id;
+ while (my $docsum = $esummary->next_DocSum) {
+ my $item = $docsum->get_Item_by_name('Name');
+ if (lc($item->get_content) eq lc($gene_name)) {
+ $ncbi_id = $docsum->get_id;
last;
}
}
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6 Build.PL
@@ -7,9 +7,9 @@
use strict;
my $v = '1.005009_002';
-eval "use Bio::Root::Build $v";
+eval "use Bio::Root::Build $v"; # min. core version required
if ($@) {
- # using die so wrappers can catch the error message
+ # using die so wrappers can catch the error message
die "BioPerl minimal core version $v is required for BioPerl-run\n";
}
@@ -23,7 +23,7 @@ my $build = Bio::Root::Build->new(
license => 'perl',
requires => {
'perl' => '5.6.1',
- #'Bio::Root::Version' => '1.007000' # checked above
+ #'Bio::Root::Version' => '1.006000' # checked above
},
recommends => {
'Algorithm::Diff' => '0/generating consensus protein family descriptions/Bio::Tools::Run::TribeMCL',
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1  INSTALL.PROGRAMS
@@ -2,7 +2,6 @@ INSTALL.PROGRAMS:
The Bioperl-run package has (Bio)perl wrappers written for the following applications:
-
1. Coils - Prediction of Coiled Coil Regions in Proteins
Bio::Tools::Run::Coil
http://www.ch.embnet.org/software/COILS_form.html
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1  INSTALL.SKIP
@@ -0,0 +1 @@
+ConfigData\.\S+$
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17 t/AnalysisFactory_soap.t
@@ -7,7 +7,8 @@ use strict;
BEGIN {
use Bio::Root::Test;
- test_begin(-tests => 12);
+ test_begin(-tests => 13,
+ -requires_networking => 1);
use_ok('Bio::Tools::Run::AnalysisFactory');
}
@@ -29,7 +30,7 @@ throws_ok { Bio::Tools::Run::AnalysisFactory->new(-access=>'non_existing') } qr/
# Now onto the nitty gritty tests of the modules methods
SKIP: {
- test_skip(-tests => 8, -requires_module => 'SOAP::Lite');
+ test_skip(-tests => 9, -requires_module => 'SOAP::Lite');
use_ok('SOAP::Lite');
my $array_ref = $factory->available_categories;
@@ -44,12 +45,8 @@ SKIP: {
isa_ok( $array_ref, 'ARRAY' );
ok( grep(/seqret/i, @$array_ref), 'available_analyses("edit") returned something' );
- TODO: {
- local $TODO = 'create_analysis() is failing';
- eval {
- my $service = $factory->create_analysis('edit.seqret');
- isa_ok( $service, 'Bio::Tools::Run::Analysis::soap' );
- };
- ok (!$@) || diag("create_analysis failed :$@");
- }
+ my $service;
+ lives_ok {$service = $factory->create_analysis('edit.seqret')};
+ skip ("create_analysis failed :$@", 1) if $@;
+ isa_ok( $service, 'Bio::Tools::Run::Analysis::soap' );
}
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3  t/Analysis_soap.t
@@ -7,7 +7,8 @@ use strict;
BEGIN {
use Bio::Root::Test;
- test_begin(-tests => 17);
+ test_begin(-tests => 17,
+ -requires_networking => 1);
use_ok('Bio::Tools::Run::Analysis');
use_ok('File::Spec');
}
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