requires 'Catalyst::TraitFor::Controller::reCAPTCHA';
requires 'LWP::Protocol::https';
##
+requires 'File::Which';
+requires 'List::Util';
requires 'Moose';
requires 'TryCatch';
requires 'namespace::autoclean';
public => $tradition->public || 0,
owner => $tradition->user ? $tradition->user->email : undef,
witnesses => [ map { $_->sigil } $tradition->witnesses ],
+ # TODO Send them all with appropriate parameters so that the
+ # client side can choose what to display.
+ reltypes => [ map { $_->name } grep { !$_->is_weak && $_->is_colocation }
+ $tradition->collation->relationship_types ]
};
## TODO Make these into callbacks in the other controllers maybe?
if( $tradition->can('language') ) {
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;
function query_stemweb_progress() {
var requrl = _get_url([ "stemweb", "query", selectedTextInfo.stemweb_jobid ]);
$.getJSON( requrl, function (data) {
- // Look for a status message, either success, running, or notfound.
- if( data.status === 'success' ) {
- // Add the new stemmata to the textinfo and tell the user.
- selectedTextInfo.stemweb_jobid = 0;
- if( data.stemmata.length > 0 ) {
- stemmata = stemmata.concat( data.stemmata );
- if( selectedStemmaID == -1 ) {
- // We have a stemma for the first time; load the first one.
- load_stemma( 0, true );
- } else {
- // Move to the index of the first added stemma.
- var newIdx = stemmata.length - data.stemmata.length;
- load_stemma( newIdx, true );
- }
- alert( 'You have one or more new stemmata!' );
+ process_stemweb_result( data );
+ });
+}
+
+function process_stemweb_result(data) {
+ // Look for a status message, either success, running, or notfound.
+ if( data.status === 'success' ) {
+ // Add the new stemmata to the textinfo and tell the user.
+ selectedTextInfo.stemweb_jobid = 0;
+ if( data.stemmata.length > 0 ) {
+ stemmata = stemmata.concat( data.stemmata );
+ if( selectedStemmaID == -1 ) {
+ // We have a stemma for the first time; load the first one.
+ load_stemma( 0, true );
} else {
- alert( 'Stemweb run finished with no stemmata...huh?!' );
+ // Move to the index of the first added stemma.
+ var newIdx = stemmata.length - data.stemmata.length;
+ load_stemma( newIdx, true );
}
- } else if( data.status === 'running' ) {
- // Just tell the user.
- alert( 'Your Stemweb query is still running!' );
- } else if( data.status === 'notfound' ) {
- // Ask the user to refresh, for now.
- alert( 'Your Stemweb query probably finished and reported back. Please reload to check.' );
+ alert( 'You have one or more new stemmata!' );
+ } else {
+ alert( 'Stemweb run finished with no stemmata...huh?!' );
}
- });
+ } else if( data.status === 'running' ) {
+ // Just tell the user.
+ alert( 'Your Stemweb query is still running!' );
+ } else if( data.status === 'notfound' ) {
+ // Ask the user to refresh, for now.
+ alert( 'Your Stemweb query probably finished and reported back. Please reload to check.' );
+ }
}
// Load the SVG we are given
buttons: {
Save: function (evt) {
$("#edit_textinfo_status").empty();
- $(evt.target).button("disable");
+ $(evt.target).closest('button').button("disable");
var requrl = _get_url([ "textinfo", selectedTextID ]);
var reqparam = $('#edit_textinfo').serialize();
$.post( requrl, reqparam, function (data) {
selectedTextInfo = data;
load_textinfo();
// Reenable the button and close the form
- $(evt.target).button("enable");
+ $(evt.target).closest('button').button("enable");
$('#textinfo-edit-dialog').dialog('close');
}, 'json' );
},
buttons: {
Save: function (evt) {
$("#edit_stemma_status").empty();
- $(evt.target).button("disable");
+ $(evt.target).closest('button').button("disable");
var stemmaseq = $('#stemmaseq').val();
var requrl = _get_url([ "stemma", selectedTextID, stemmaseq ]);
var reqparam = { 'dot': $('#dot_field').val() };
// Display the new stemma
load_stemma( selectedStemmaID, true );
// Reenable the button and close the form
- $(evt.target).button("enable");
+ $(evt.target).closest('button').button("enable");
$('#stemma-edit-dialog').dialog('close');
}, 'json' );
},
$('#stemweb-ui-dialog').dialog({
autoOpen: false,
height: 160,
- width: 225,
+ width: 240,
modal: true,
buttons: {
Run: function (evt) {
$("#stemweb_run_status").empty();
- $(evt.target).button("disable");
+ $(evt.target).closest('button').button("disable");
var requrl = _get_url([ "stemweb", "request" ]);
var reqparam = $('#call_stemweb').serialize();
// TODO We need to stash the literal SVG string in stemmata
// somehow. Implement accept header on server side to decide
// whether to send application/json or application/xml?
$.getJSON( requrl, reqparam, function (data) {
- // Job ID is in data.jobid. TODO do something with it.
- selectedTextInfo.stemweb_jobid = data.jobid;
- $(evt.target).button("enable");
+ $(evt.target).closest('button').button("enable");
$('#stemweb-ui-dialog').dialog('close');
- // Reload the current stemma to rejigger the buttons
- load_stemma( selectedStemmaID, true );
+ if( 'jobid' in data ) {
+ // There is a pending job.
+ selectedTextInfo.stemweb_jobid = data.jobid;
+ alert("Your request has been submitted to Stemweb.\nThe resulting tree will appear in due course.");
+ // Reload the current stemma to rejigger the buttons
+ load_stemma( selectedStemmaID, true );
+ } else {
+ // We appear to have an answer; process it.
+ process_stemweb_result( data );
+ }
}, 'json' );
},
Cancel: function() {
open: function(evt) {
$('#stemweb_run_status').empty();
$('#stemweb_tradition').attr('value', selectedTextID );
+ $('#stemweb_merge_reltypes').empty();
+ $.each( selectedTextInfo.reltypes, function( i, r ) {
+ var relation_opt = $('<option>').attr( 'value', r ).append( r );
+ $('#stemweb_merge_reltypes').append( relation_opt );
+ });
+ $('#stemweb_merge_reltypes').multiselect({
+ header: false,
+ selectedList: 3
+ });
},
}).ajaxError( function(event, jqXHR, ajaxSettings, thrownError) {
$(event.target).parent().find('.ui-button').button("enable");
<select id="stemweb_algorithm" name="algorithm"></select><br/>
<!-- Algorithm-specific options, if any, will be added within this div -->
<div id="stemweb_runtime_options"></div>
+ <br/>
+ <!-- Options applicable to all algorithms belong within this div -->
+ <div id="stemweb_local_options">
+ <label for="merge_reltypes">Disregard variation of type:</label>
+ <select multiple name="merge_reltypes" id="stemweb_merge_reltypes"></select>
+ </div>
</form>
<div id="stemweb_run_status"></div>
</div>
projects / scpubgit/stemmaweb.git / commitdiff