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;
BEGIN { extends 'Catalyst::Controller' }
-## TODO Move the /algorithms/available function to the Stemweb module
-my $STEMWEB_BASE_URL = 'http://slinkola.users.cs.helsinki.fi';
+has stemweb_url => (
+ is => 'ro',
+ 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
POST stemweb/result
Content-Type: application/json
(On success):
- { job_id: <ID number>
+ { jobid: <ID number>
status: 0
format: <format>
result: <data> }
my $answer;
if( ref( $c->request->body ) eq 'File::Temp' ) {
# Read in the file and parse that.
- open( POSTDATA, $c->request->body ) or die "Failed to open post data file";
+ $c->log->debug( "Request body is in a temp file" );
+ open( POSTDATA, $c->request->body )
+ or return _json_error( $c, 500, "Failed to open post data file" );
binmode( POSTDATA, ':utf8' );
# JSON should be all one line
my $pdata = <POSTDATA>;
} else {
$answer = from_json( $c->request->body );
}
+ $c->log->debug( "Received push notification from Stemweb: "
+ . to_json( $answer ) );
return _process_stemweb_result( $c, $answer );
} else {
return _json_error( $c, 403, 'Please use POST!' );
}
}
+=head2 available
+
+ GET algorithms/available
+
+Queries the Stemweb server for available stemma generation algorithms and their
+parameters. Returns the JSON answer as obtained from Stemweb.
+
+=cut
+
+sub available :Local :Args(0) {
+ my( $self, $c ) = @_;
+ my $ua = LWP::UserAgent->new();
+ my $resp = $ua->get( $self->stemweb_url . '/algorithms/available' );
+ if( $resp->is_success ) {
+ 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'} = {};
+ }
+ $c->forward('View::JSON');
+}
+
=head2 query
GET stemweb/query/<jobid>
sub query :Local :Args(1) {
my( $self, $c, $jobid ) = @_;
my $ua = LWP::UserAgent->new();
- my $resp = $ua->get( $STEMWEB_BASE_URL . "/algorithms/jobstatus/$jobid" );
+ my $resp = $ua->get( $self->stemweb_url . "/algorithms/jobstatus/$jobid" );
if( $resp->is_success ) {
# Process it
my $response = decode_utf8( $resp->content );
## Helper function for parsing Stemweb result data either by push or by pull
sub _process_stemweb_result {
my( $c, $answer ) = @_;
- # Find a tradition with the defined Stemweb job ID.
- # TODO: Maybe get Stemweb to pass back the tradition ID...
+ # Find the specified tradition and check its job ID.
my $m = $c->model('Directory');
- my @traditions;
- ## STUPID HACK: unless we load the possible tradition owners
- ## within scope of the scan, they will not exist when the affected
- ## tradition is saved.
- my @users;
- $m->scan( sub{ push( @traditions, $_[0] )
- if $_[0]->$_isa('Text::Tradition')
- && $_[0]->has_stemweb_jobid
- && $_[0]->stemweb_jobid eq $answer->{job_id};
- push( @users, $_[0] ) if $_[0]->$_isa('Text::Tradition::User');
- } );
- if( @traditions == 1 ) {
- my $tradition = shift @traditions;
- if( $answer->{status} == 0 ) {
- my $stemmata;
+ my $tradition = $m->tradition( $answer->{textid} );
+ unless( $tradition ) {
+ return _json_error( $c, 400, "No tradition found with ID "
+ . $answer->{textid} );
+ }
+ if( $answer->{status} == 0 ) {
+ my $stemmata;
+ if( $tradition->has_stemweb_jobid
+ && $tradition->stemweb_jobid eq $answer->{jobid} ) {
try {
$stemmata = $tradition->record_stemweb_result( $answer );
$m->save( $tradition );
} catch {
return _json_error( $c, 500, $@ );
}
+ } else {
+ # It may be that we already received a callback meanwhile.
+ # Check all stemmata for the given jobid and return them.
+ @$stemmata = grep { $_->came_from_jobid && $_->from_jobid eq $answer->{jobid} } $tradition->stemmata;
+ }
+ if( @$stemmata ) {
# If we got here, success!
+ # TODO Use helper in Root.pm to do this
my @steminfo = map { {
name => $_->identifier,
directed => _json_bool( !$_->is_undirected ),
$c->stash->{'result'} = {
'status' => 'success',
'stemmata' => \@steminfo };
- } elsif( $answer->{status} < 1 ) {
- $c->stash->{'result'} = { 'status' => 'running' };
} else {
- return _json_error( $c, 500,
- "Stemweb failure not handled: " . $answer->{result} );
+ # Hm, no stemmata found on this tradition with this jobid.
+ # Clear the tradition jobid so that the user can try again.
+ if( $tradition->has_stemweb_jobid ) {
+ $tradition->_clear_stemweb_jobid;
+ $m->save( $tradition );
+ }
+ $c->stash->{'result'} = { status => 'notfound' };
}
- } elsif( @traditions ) {
- return _json_error( $c, 500,
- "Multiple traditions with Stemweb job ID " . $answer->{job_id} . "!" );
+ } elsif( $answer->{status} == 1 ) {
+ $c->stash->{'result'} = { 'status' => 'running' };
} else {
- # Possible that the tradition got updated in the meantime...
- if( $answer->{status} == 0 ) {
- $c->stash->{'result'} = { 'status' => 'notfound' };
- } else {
- return _json_error( $c, 400,
- "No tradition found with Stemweb job ID " . $answer->{job_id} );
- }
+ return _json_error( $c, 500,
+ "Stemweb failure not handled: " . $answer->{result} );
}
$c->forward('View::JSON');
}
'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,
- userid => $c->user->get_object->email,
- parameters => $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( $STEMWEB_BASE_URL . "/algorithms/process/$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 _json_error( $c, 403, 'You do not have permission to view this tradition.' );
}
+# QUICK HACK to deal with strict Stemweb validation.
+sub _cast_nonstrings {
+ my $params = shift;
+ foreach my $k ( keys %$params ) {
+ my $v = $params->{$k};
+ if( looks_like_number( $v ) ) {
+ $params->{$k} = $v * 1;
+ } elsif ( !defined $v || $v eq 'true' ) {
+ $params->{$k} = _json_bool( $v );
+ }
+ }
+ return $params;
+}
+
# Helper to throw a JSON exception
sub _json_error {
my( $c, $code, $errmsg ) = @_;
$c->stash->{'result'} = { 'error' => $errmsg };
$c->forward('View::JSON');
return 0;
-}
+}
sub _json_bool {
return $_[0] ? JSON::true : JSON::false;
}
+sub _has_pars {
+ my $self = shift;
+ return $self->pars_path || which('pars');
+}
+
1;
projects / scpubgit/stemmaweb.git / blobdiff