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Merge pull request #102 from sanger-pathogens/update_api_endpoints
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Update api endpoints
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@blue-moon22
blue-moon22 authored Sep 1, 2021
2 parents db79bac + 44a1361 commit add2fb7
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Showing 21 changed files with 40 additions and 40 deletions.
2 changes: 1 addition & 1 deletion config/ena_data_submission.conf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
'webin_user' => 'username',
'webin_pass' => 'password',
'ena_base_path' => 'http://www.ebi.ac.uk/ena/data/view/',
'ena_base_path' => 'http://www.ebi.ac.uk/ena/browser/api/xml/',
'pubmed_url_base' => 'http://www.ncbi.nlm.nih.gov/pubmed/?term=',
'taxon_lookup_service' => 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&report=xml&id=',
'output_root' => '/nfs/pathogen/ena_updates/',
Expand Down
6 changes: 3 additions & 3 deletions lib/Bio/ENA/DataSubmission/AccessionConverter.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ sub convert_secondary_project_accession_to_primary {
my ($self, $accession) = @_;

if (defined($accession) && $accession =~ /ERP/) {
my $xml = Bio::ENA::DataSubmission::XML->new(url => $self->ena_base_path . "$accession&display=xml", ena_base_path => $self->ena_base_path)->parse_from_url;
my $xml = Bio::ENA::DataSubmission::XML->new(url => $self->ena_base_path . "$accession", ena_base_path => $self->ena_base_path)->parse_from_url;
if (defined($xml) &&
defined($xml->{STUDY}) &&
defined($xml->{STUDY}->[0]) &&
Expand All @@ -44,7 +44,7 @@ sub convert_secondary_project_accession_to_primary {
sub convert_secondary_sample_accession_to_biosample {
my ($self, $accession) = @_;
if (defined($accession) && $accession =~ /ERS/) {
my $xml = Bio::ENA::DataSubmission::XML->new(url => $self->ena_base_path . "$accession&display=xml", ena_base_path => $self->ena_base_path)->parse_from_url;
my $xml = Bio::ENA::DataSubmission::XML->new(url => $self->ena_base_path . "$accession", ena_base_path => $self->ena_base_path)->parse_from_url;
if (defined($xml) &&
defined($xml->{SAMPLE}) &&
defined($xml->{SAMPLE}->[0]) &&
Expand All @@ -62,4 +62,4 @@ sub convert_secondary_sample_accession_to_biosample {

__PACKAGE__->meta->make_immutable;
no Moose;
1;
1;
12 changes: 6 additions & 6 deletions lib/Bio/ENA/DataSubmission/CommandLine/CompareMetadata.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ Bio::ENA::DataSubmission::CommandLine::CompareMetadata
=head1 SYNOPSIS
use Bio::ENA::DataSubmission::CommandLine::CompareMetadata;
1. pull XML from ENA using http://www.ebi.ac.uk/ena/data/view/ERS*****&display=xml
1. pull XML from ENA using http://www.ebi.ac.uk/ena/browser/api/xml/ERS*****
2. parse to data structure
3. parse manifest to same data structure
4. compare data structures
Expand Down Expand Up @@ -65,7 +65,7 @@ sub BUILD {
$self->manifest($file) if ( defined $file );
$self->outfile($outfile) if ( defined $outfile );
$self->help($help) if ( defined $help );

$self->config_file($config_file) if ( defined $config_file );
( -e $self->config_file ) or Bio::ENA::DataSubmission::Exception::FileNotFound->throw( error => "Cannot find config file\n" );
$self->_populate_attributes_from_config_file;
Expand All @@ -81,7 +81,7 @@ sub _populate_attributes_from_config_file
}

sub check_inputs{
my $self = shift;
my $self = shift;
return(
$self->manifest
&& !$self->help
Expand Down Expand Up @@ -155,7 +155,7 @@ sub _report{
unshift(@data, ['Total Conflicts', $#data]);
}
else{
unshift(@data, ['Total Conflicts', 0]);
unshift(@data, ['Total Conflicts', 0]);
}
my $xls = Bio::ENA::DataSubmission::Spreadsheet->new( data => \@data, outfile => $outfile );
$xls->write_xls;
Expand All @@ -174,4 +174,4 @@ USAGE

__PACKAGE__->meta->make_immutable;
no Moose;
1;
1;
16 changes: 8 additions & 8 deletions lib/Bio/ENA/DataSubmission/CommandLine/ValidateAnalysisManifest.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ Bio::ENA::DataSubmission::CommandLine::ValidateManifest
=head1 SYNOPSIS
use Bio::ENA::DataSubmission::CommandLine::ValidateManifest;
=head1 METHODS
Expand Down Expand Up @@ -53,7 +53,7 @@ has 'outfile' => ( is => 'rw', isa => 'Str', required => 0 );
has 'edit' => ( is => 'rw', isa => 'Bool', required => 0 );
has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
has '_filetypes' => ( is => 'rw', isa => 'ArrayRef', required => 0, lazy_build => 1 );
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/data/view/');
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/browser/api/xml/');
has 'pubmed_url_base' => ( is => 'rw', isa => 'Str', default => 'http://www.ncbi.nlm.nih.gov/pubmed/?term=');

has 'config_file' => ( is => 'rw', isa => 'Str', required => 0, default => $ENV{'ENA_SUBMISSIONS_CONFIG'});
Expand Down Expand Up @@ -106,7 +106,7 @@ sub _populate_attributes_from_config_file
}

sub check_inputs{
my $self = shift;
my $self = shift;
return(
$self->file
&& !$self->help
Expand Down Expand Up @@ -162,7 +162,7 @@ sub run {
for my $c ( 0..$#row ) {
my $cell = $row[$c];
if ( defined $cell ){
my $gen_error = Bio::ENA::DataSubmission::Validator::Error::General->new(
my $gen_error = Bio::ENA::DataSubmission::Validator::Error::General->new(
identifier => $name,
cell => $cell,
field => $header[$c]
Expand All @@ -175,8 +175,8 @@ sub run {

# mandatory cells
my $mandatory = [ 0, 1, 2, 3, 4, 6, 7, 9, 10, 11 ];
my $mandatory_error = Bio::ENA::DataSubmission::Validator::Error::MandatoryCells->new(
row => \@row,
my $mandatory_error = Bio::ENA::DataSubmission::Validator::Error::MandatoryCells->new(
row => \@row,
mandatory => $mandatory
)->validate;
push( @errors_found, $mandatory_error ) if ( $mandatory_error->triggered );
Expand Down Expand Up @@ -274,7 +274,7 @@ sub run {
push( @errors_found, $pubmed_id_error ) if ( $pubmed_id_error->triggered );
}
}

#--------------#
# write report #
#--------------#
Expand All @@ -289,7 +289,7 @@ sub run {
# edit/fix where possible #
#-------------------------#


return (scalar(@errors_found) > 0) ? 0 : 1;
}

Expand Down
4 changes: 2 additions & 2 deletions lib/Bio/ENA/DataSubmission/CommandLine/ValidateManifest.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ Bio::ENA::DataSubmission::CommandLine::ValidateManifest
=head1 SYNOPSIS
use Bio::ENA::DataSubmission::CommandLine::ValidateManifest;
=head1 METHODS
Expand Down Expand Up @@ -52,7 +52,7 @@ has 'edit' => (is => 'rw', isa => 'Bool', required => 0);
has 'help' => (is => 'rw', isa => 'Bool', required => 0);
has 'config_file' => (is => 'rw', isa => 'Maybe[Str]', required => 0, default => $ENV{'ENA_SUBMISSIONS_CONFIG'});

has 'ena_base_path' => (is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/data/view/');
has 'ena_base_path' => (is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/browser/api/xml/');
has 'taxon_lookup_service' => (is => 'rw', isa => 'Str', default => 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=taxonomy&report=xml&id=');
has 'data_root' => (is => 'ro', isa => 'Maybe[Str]', required => 0, default => $ENV{'ENA_SUBMISSIONS_DATA'});
has 'valid_countries_file' => (is => 'ro', isa => 'Str', , lazy => 1, builder => '_build_valid_countries_file');
Expand Down
12 changes: 6 additions & 6 deletions lib/Bio/ENA/DataSubmission/Validator/Error/ProjectAccession.pm
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Expand Up @@ -15,7 +15,7 @@ use Bio::ENA::DataSubmission::XML;

has 'accession' => ( is => 'ro', isa => 'Str', required => 1 );
has 'identifier' => ( is => 'ro', isa => 'Str', required => 1 );
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/data/view/');
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/browser/api/xml/');

sub validate {
my $self = shift;
Expand All @@ -24,9 +24,9 @@ sub validate {

if( $acc =~ m/^ERP/ || $acc =~ m/^SRP/ || $acc =~ m/^PRJ/ ){
# pull XML from ENA and verify that it isn't empty
my $xml = Bio::ENA::DataSubmission::XML->new( url => $self->ena_base_path."$acc&display=xml",ena_base_path => $self->ena_base_path )->parse_from_url;
$self->set_error_message( $id, "Invalid study accession - could not be found at the ENA" ) if( !(defined $xml->{STUDY} || defined $xml->{PROJECT}) );
my $xml = Bio::ENA::DataSubmission::XML->new( url => $self->ena_base_path."$acc",ena_base_path => $self->ena_base_path )->parse_from_url;

$self->set_error_message( $id, "Invalid study accession - could not be found at the ENA" ) if( !(defined $xml->{STUDY} || defined $xml->{PROJECT}) );
}
else {
$self->set_error_message( $id, "Invalid study accession - must take format ERPxxxxx, SRPxxxxx or PRJxxxx" );
Expand All @@ -37,9 +37,9 @@ sub validate {
}

sub fix_it {

}

no Moose;
__PACKAGE__->meta->make_immutable;
1;
1;
10 changes: 5 additions & 5 deletions lib/Bio/ENA/DataSubmission/Validator/Error/RunAccession.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ use Bio::ENA::DataSubmission::XML;

has 'accession' => ( is => 'ro', isa => 'Str', required => 1 );
has 'identifier' => ( is => 'ro', isa => 'Str', required => 1 );
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/data/view/');
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/browser/api/xml/');

sub validate {
my $self = shift;
Expand All @@ -24,8 +24,8 @@ sub validate {

if( $acc =~ m/^ERR/ || $acc =~ m/^SRR/){
# pull XML from ENA and verify that it isn't empty
my $xml = Bio::ENA::DataSubmission::XML->new( url => $self->ena_base_path."$acc&display=xml",ena_base_path => $self->ena_base_path )->parse_from_url;
$self->set_error_message( $id, "Invalid run accession - could not be found at the ENA" ) unless ( defined $xml->{RUN} );
my $xml = Bio::ENA::DataSubmission::XML->new( url => $self->ena_base_path."$acc",ena_base_path => $self->ena_base_path )->parse_from_url;
$self->set_error_message( $id, "Invalid run accession - could not be found at the ENA" ) unless ( defined $xml->{RUN} );
}
else {
$self->set_error_message( $id, "Invalid run accession - must take format ERRxxxxx or SRRxxxxx" );
Expand All @@ -36,9 +36,9 @@ sub validate {
}

sub fix_it {

}

no Moose;
__PACKAGE__->meta->make_immutable;
1;
1;
10 changes: 5 additions & 5 deletions lib/Bio/ENA/DataSubmission/Validator/Error/SampleAccession.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ use Bio::ENA::DataSubmission::XML;

has 'accession' => ( is => 'ro', isa => 'Str', required => 1 );
has 'identifier' => ( is => 'ro', isa => 'Str', required => 1 );
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/data/view/');
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/browser/api/xml/');

sub validate {
my $self = shift;
Expand All @@ -24,8 +24,8 @@ sub validate {

if( $acc =~ m/^ERS/ || $acc =~ m/^SAM/ || $acc =~ m/^SRS/){
# pull XML from ENA and verify that it isn't empty
my $xml = Bio::ENA::DataSubmission::XML->new( url => $self->ena_base_path."$acc&display=xml",ena_base_path => $self->ena_base_path )->parse_from_url;
$self->set_error_message( $id, "Invalid sample accession - could not be found at the ENA" ) unless ( defined $xml->{SAMPLE} );
my $xml = Bio::ENA::DataSubmission::XML->new( url => $self->ena_base_path."$acc",ena_base_path => $self->ena_base_path )->parse_from_url;
$self->set_error_message( $id, "Invalid sample accession - could not be found at the ENA" ) unless ( defined $xml->{SAMPLE} );
}
else {
$self->set_error_message( $id, "Invalid sample accession - must take format ERSxxxx, SAMxxxx, or SRSxxxxx" );
Expand All @@ -36,9 +36,9 @@ sub validate {
}

sub fix_it {

}

no Moose;
__PACKAGE__->meta->make_immutable;
1;
1;
8 changes: 4 additions & 4 deletions lib/Bio/ENA/DataSubmission/XML.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ Bio::ENA::DataSubmission::XML
=head1 SYNOPSIS
use Bio::ENA::DataSubmission::XML;
=head1 METHODS
Expand Down Expand Up @@ -47,7 +47,7 @@ has 'outfile' => ( is => 'rw', isa => 'Str', required
has 'root' => ( is => 'ro', isa => 'Str', required => 0, default => 'root' );
has '_fields' => ( is => 'rw', isa => 'ArrayRef', required => 0, lazy_build => 1 );
has 'validation_report' => ( is => 'rw', isa => 'XML::LibXML::Error', required => 0 );
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/data/view/' );
has 'ena_base_path' => ( is => 'rw', isa => 'Str', default => 'http://www.ebi.ac.uk/ena/browser/api/xml/' );
has 'proxy' => ( is => 'rw', isa => 'Str', default => 'http://wwwcache.sanger.ac.uk:3128' );
has 'attributes_to_delete' => (
is => 'ro',
Expand Down Expand Up @@ -108,7 +108,7 @@ sub update_sample {

my $acc = $sample->{'sample_accession'};
( defined $acc ) or Bio::ENA::DataSubmission::Exception::InvalidInput->throw( error => "Accession number data not present\n" );
$self->url( $self->ena_base_path . "$acc&display=xml" );
$self->url( $self->ena_base_path . "$acc" );

my $xml = $self->parse_from_url;

Expand Down Expand Up @@ -244,7 +244,7 @@ sub parse_from_url {
sub parse_xml_metadata {
my ( $self, $acc ) = @_;

$self->url( $self->ena_base_path . $acc . "&display=xml" );
$self->url( $self->ena_base_path . $acc );
my $xml = $self->parse_from_url;
my @fields = @{ $self->_fields };

Expand Down
0 t/data/ERP001039&display=xml → t/data/ERP001039
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0 t/data/ERR363472&display=xml → t/data/ERR363472
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0 t/data/ERR369155&display=xml → t/data/ERR369155
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0 t/data/ERR369164&display=xml → t/data/ERR369164
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0 t/data/ERS001491&display=xml → t/data/ERS001491
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0 t/data/ERS002783&display=xml → t/data/ERS002783
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0 t/data/ERS023435&display=xml → t/data/ERS023435
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0 t/data/ERS092760&display=xml → t/data/ERS092760
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0 t/data/ERS311393&display=xml → t/data/ERS311393
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0 t/data/ERS311489&display=xml → t/data/ERS311489
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0 t/data/ERS311560&display=xml → t/data/ERS311560
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0 t/data/ERS486637&display=xml → t/data/ERS486637
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