X-Git-Url: http://git.shadowcat.co.uk/gitweb/gitweb.cgi?a=blobdiff_plain;f=lib%2Fstemmaweb%2FController%2FStemweb.pm;h=c37b600bd7ccd01db1818eb47ef959f8882f00c4;hb=3cb9d9c0bc6a0c24d413b04900b7c567964af280;hp=f0ffa087f12c759d5ca1b4be09261aebd94bb10b;hpb=7074436718faf60f0a173d439f8db2ca97de2e3b;p=scpubgit%2Fstemmaweb.git

diff --git a/lib/stemmaweb/Controller/Stemweb.pm b/lib/stemmaweb/Controller/Stemweb.pm
index f0ffa08..c37b600 100644
--- a/lib/stemmaweb/Controller/Stemweb.pm
+++ b/lib/stemmaweb/Controller/Stemweb.pm
@@ -1,16 +1,34 @@
 package stemmaweb::Controller::Stemweb;
 use Moose;
 use namespace::autoclean;
-use JSON qw/ from_json /;
+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
 
@@ -28,7 +46,7 @@ L<https://docs.google.com/document/d/1aNYGAo1v1WPDZi6LXZ30FJSMJwF8RQPYbOkKqHdCZE
  POST stemweb/result
  Content-Type: application/json
  (On success):
- { job_id: <ID number>
+ { jobid: <ID number>
    status: 0
    format: <format>
    result: <data> }
@@ -49,53 +67,160 @@ sub result :Local :Args(0) {
 		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>;
 			chomp $pdata;
 			close POSTDATA;
-			$answer = from_json( $pdata );
+			try {
+				$answer = from_json( $pdata );
+			} catch {
+				return _json_error( $c, 400, 
+					"Could not parse POST request '' $pdata '' as JSON: $@" );
+			}
 		} else {
 			$answer = from_json( $c->request->body );
 		}
-		# Find a tradition with the defined Stemweb job ID.
-		# TODO: Maybe get Stemweb to pass back the tradition ID...
-		my $m = $c->model('Directory');
-		my @traditions;
-		$m->scan( sub{ push( @traditions, $_[0] )
-						if $_[0]->$_isa('Text::Tradition')
-						&& $_[0]->has_stemweb_jobid 
-						&& $_[0]->stemweb_jobid eq $answer->{job_id}; 
-					} );
-		if( @traditions == 1 ) {
-			my $tradition = shift @traditions;
-			if( $answer->{status} == 0 ) {
-				try {
-					$tradition->record_stemweb_result( $answer );
-					$m->save( $tradition );
-				} catch( Text::Tradition::Error $e ) {
-					return _json_error( $c, 500, $e->message );
-				} catch {
-					return _json_error( $c, 500, $@ );
+		$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'
 				}
-				# If we got here, success!
-				$c->stash->{'result'} = { 'status' => 'success' };
-				$c->forward('View::JSON');
-			} else {
-				return _json_error( $c, 500,
-					"Stemweb failure not handled: " . $answer->{result} );
-			}
-		} elsif( @traditions ) {
+			});
+		}
+		$c->stash->{'result'} = $parameters;
+	} else {
+		$c->stash->{'result'} = {};
+	}
+	$c->forward('View::JSON');
+}
+
+=head2 query
+
+ GET stemweb/query/<jobid>
+
+A backup method to query the stemweb server to check a particular job status.
+Returns a result as in /stemweb/result above, but status can also be -1 to 
+indicate that the job is still running.
+
+=cut
+
+sub query :Local :Args(1) {
+	my( $self, $c, $jobid ) = @_;
+	my $ua = LWP::UserAgent->new();
+	my $resp = $ua->get( $self->stemweb_url . "/algorithms/jobstatus/$jobid" );
+	if( $resp->is_success ) {
+		# Process it
+		my $response = decode_utf8( $resp->content );
+		$c->log->debug( "Got a response from the server: $response" );
+		my $answer;
+		try {
+			$answer = from_json( $response );
+		} catch {
 			return _json_error( $c, 500, 
-				"Multiple traditions with Stemweb job ID " . $answer->{job_id} . "!" );
+				"Could not parse stemweb response '' $response '' as JSON: $@" );
+		}
+		return _process_stemweb_result( $c, $answer );
+	} 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 );
+	}
+}
+
+
+## Helper function for parsing Stemweb result data either by push or by pull
+sub _process_stemweb_result {
+	my( $c, $answer ) = @_;
+	# Find the specified tradition and check its job ID.
+	my $m = $c->model('Directory');
+	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( Text::Tradition::Error $e ) {
+				return _json_error( $c, 500, $e->message );
+			} catch {
+				return _json_error( $c, 500, $@ );
+			}
 		} else {
-			return _json_error( $c, 400, 
-				"No tradition found with Stemweb job ID " . $answer->{job_id} );
+			# It may be that we already received a callback meanwhile.
+			# Check all stemmata for the given jobid and return them.
+			@$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 ),
+					svg => $_->as_svg() } } 
+				@$stemmata;
+			$c->stash->{'result'} = { 
+				'status' => 'success',
+				'stemmata' => \@steminfo };
+		} else {
+			# 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( $answer->{status} == 1 ) {
+		$c->stash->{'result'} = { 'status' => 'running' };
 	} else {
-		return _json_error( $c, 403, 'Please use POST!' );
+		return _json_error( $c, 500,
+			"Stemweb failure not handled: " . $answer->{result} );
 	}
+	$c->forward('View::JSON');
 }
 
 =head2 request
@@ -122,39 +247,72 @@ sub request :Local :Args(0) {
 			'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->email,
-		parameters => $reqparams };
-		
-	# Call to the appropriate URL with the request parameters.
-	my $ua = LWP::UserAgent->new();
-	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
-		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->status . " / "
-			. $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 );
+		}
 	}
 }
 
@@ -174,6 +332,20 @@ sub _check_permission {
 	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 ) = @_;
@@ -181,6 +353,16 @@ sub _json_error {
 	$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;
\ No newline at end of file
+
+1;