use Moose;
use namespace::autoclean;
use Encode qw/ decode_utf8 /;
+use File::Which;
use JSON;
+use List::Util qw/ max /;
use LWP::UserAgent;
use Safe::Isa;
use Scalar::Util qw/ looks_like_number /;
+use Text::Tradition::StemmaUtil qw/ character_input phylip_pars /;
use TryCatch;
use URI;
isa => 'Str',
default => 'http://slinkola.users.cs.helsinki.fi',
);
+
+has pars_path => (
+ is => 'ro',
+ isa => 'Str',
+ );
+
+has pars_pk => (
+ is => 'rw',
+ isa => 'Int',
+ );
=head1 NAME
my $ua = LWP::UserAgent->new();
my $resp = $ua->get( $self->stemweb_url . '/algorithms/available' );
if( $resp->is_success ) {
- $c->stash->{'result'} = decode_json( $resp->content );
+ my $parameters = decode_json( $resp->content );
+ # Temporary hack: add Pars
+ if( $self->_has_pars ) {
+ # Use the highest passed primary key + 1
+ my $parspk = max( map { $_->{pk} }
+ grep { $_->{model} eq 'algorithms.algorithm' } @$parameters ) + 1;
+ # Add Pars as an algorithm
+ $self->pars_pk( $parspk );
+ push( @$parameters, {
+ pk => $parspk,
+ model => 'algorithms.algorithm',
+ fields => {
+ args => [],
+ name => 'Pars'
+ }
+ });
+ }
+ $c->stash->{'result'} = $parameters;
} else {
$c->stash->{'result'} = {};
}
'You do not have permission to update stemmata for this tradition' ) )
unless $ok eq 'full';
- # Form the request for Stemweb.
my $algorithm = delete $reqparams->{algorithm};
- my $return_uri = URI->new( $c->uri_for( '/stemweb/result' ) );
- my $stemweb_request = {
- return_path => $return_uri->path,
- return_host => $return_uri->host_port,
- data => $t->collation->as_tsv({noac => 1}),
- userid => $c->user->get_object->email,
- textid => $tid,
- parameters => _cast_nonstrings( $reqparams ) };
-
- # Call to the appropriate URL with the request parameters.
- my $ua = LWP::UserAgent->new();
- $c->log->debug( 'Sending request to Stemweb: ' . to_json( $stemweb_request ) );
- my $resp = $ua->post( $self->stemweb_url . "/algorithms/process/$algorithm/",
- 'Content-Type' => 'application/json; charset=utf-8',
- 'Content' => encode_json( $stemweb_request ) );
- if( $resp->is_success ) {
- # Process it
- $c->log->debug( 'Got a response from the server: '
- . decode_utf8( $resp->content ) );
- my $stemweb_response = decode_json( $resp->content );
+ my $mergetypes = delete $reqparams->{merge_reltypes};
+ if( $self->_has_pars && $algorithm == $self->pars_pk ) {
+ my $start_time = scalar( gmtime( time() ) );
+ $t->set_stemweb_jobid( 'local' );
+ my $cdata = character_input( $t, { collapse => $mergetypes } );
+ my $newick;
try {
- $t->set_stemweb_jobid( $stemweb_response->{jobid} );
- } catch( Text::Tradition::Error $e ) {
- return _json_error( $c, 429, $e->message );
+ $newick = phylip_pars( $cdata, { parspath => $self->_has_pars } );
+ } catch ( Text::Tradition::Error $e ) {
+ return _json_error( $c, 503, "Parsimony tree generation failed: "
+ . $e->message );
}
- $c->model('Directory')->save( $t );
- $c->stash->{'result'} = $stemweb_response;
- $c->forward('View::JSON');
- } elsif( $resp->code == 500 && $resp->header('Client-Warning')
- && $resp->header('Client-Warning') eq 'Internal response' ) {
- # The server was unavailable.
- return _json_error( $c, 503, "The Stemweb server is currently unreachable." );
+ # We have a result, so form an answer to process.
+ my $answer = {
+ status => 0,
+ algorithm => 'pars',
+ 'format' => 'newick',
+ textid => $tid,
+ jobid => 'local',
+ result => $newick,
+ start_time => $start_time
+ };
+ return _process_stemweb_result( $c, $answer );
} else {
- return _json_error( $c, 500, "Stemweb error: " . $resp->code . " / "
- . $resp->content );
+ # Form the request for Stemweb.
+ my $return_uri = URI->new( $c->uri_for( '/stemweb/result' ) );
+ my $tsv_options = { noac => 1 };
+ if( $mergetypes && @$mergetypes ) {
+ $tsv_options->{mergetypes} = $mergetypes;
+ }
+ my $stemweb_request = {
+ return_path => $return_uri->path,
+ return_host => $return_uri->host_port,
+ data => $t->collation->as_tsv( $tsv_options ),
+ userid => $c->user->get_object->email,
+ textid => $tid,
+ parameters => _cast_nonstrings( $reqparams ) };
+
+ # Call to the appropriate URL with the request parameters.
+ my $ua = LWP::UserAgent->new();
+ $c->log->debug( 'Sending request to Stemweb: ' . to_json( $stemweb_request ) );
+ my $resp = $ua->post( $self->stemweb_url . "/algorithms/process/$algorithm/",
+ 'Content-Type' => 'application/json; charset=utf-8',
+ 'Content' => encode_json( $stemweb_request ) );
+ if( $resp->is_success ) {
+ # Process it
+ $c->log->debug( 'Got a response from the server: '
+ . decode_utf8( $resp->content ) );
+ my $stemweb_response = decode_json( $resp->content );
+ try {
+ $t->set_stemweb_jobid( $stemweb_response->{jobid} );
+ } catch( Text::Tradition::Error $e ) {
+ return _json_error( $c, 429, $e->message );
+ }
+ $c->model('Directory')->save( $t );
+ $c->stash->{'result'} = $stemweb_response;
+ $c->forward('View::JSON');
+ } elsif( $resp->code == 500 && $resp->header('Client-Warning')
+ && $resp->header('Client-Warning') eq 'Internal response' ) {
+ # The server was unavailable.
+ return _json_error( $c, 503, "The Stemweb server is currently unreachable." );
+ } else {
+ return _json_error( $c, 500, "Stemweb error: " . $resp->code . " / "
+ . $resp->content );
+ }
}
}
return $_[0] ? JSON::true : JSON::false;
}
+sub _has_pars {
+ my $self = shift;
+ return $self->pars_path || which('pars');
+}
+
1;
projects / scpubgit/stemmaweb.git / blobdiff