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1 | package TreeOfTexts::Controller::Stemmagraph; |
2 | use Moose; |
3 | use namespace::autoclean; |
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4 | use File::Temp; |
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5 | use JSON; |
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6 | use Text::Tradition::Collation; |
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7 | use Text::Tradition::StemmaUtil qw/ character_input phylip_pars newick_to_svg /; |
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8 | |
9 | BEGIN { extends 'Catalyst::Controller' } |
10 | |
11 | # |
12 | # Sets the actions in this controller to be registered with no prefix |
13 | # so they function identically to actions created in MyApp.pm |
14 | # |
15 | __PACKAGE__->config(namespace => ''); |
16 | |
17 | =head1 NAME |
18 | |
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19 | TreeOfTexts::Controller::Stemmagraph - Simple controller for stemma display |
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20 | |
21 | =head1 DESCRIPTION |
22 | |
23 | [enter your description here] |
24 | |
25 | =head1 METHODS |
26 | |
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27 | =cut |
28 | |
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29 | sub get_graph :Local { |
30 | my( $self, $c ) = @_; |
31 | # If called interactively, we have params 'display', 'output', 'witnesses' |
32 | # If called non-interactively, we look at headers and content. |
33 | # The body is actually a File::Temp object; this is undocumented but |
34 | # so it seems to be. |
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35 | my $dotfile; |
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36 | my $must_unlink = 0; |
37 | if( $c->request->params->{'dot'} ) { |
38 | # Make a File::Temp object. |
39 | my $tmpfile = File::Temp->new( UNLINK => 0 ); |
40 | print $tmpfile $c->request->params->{'dot'}; |
41 | $dotfile = $tmpfile->filename; |
42 | $must_unlink = 1; |
43 | } else { |
44 | $dotfile = $c->request->body; |
45 | } |
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46 | my $format = 'svg'; |
47 | |
48 | # Render the dot in the given format. |
49 | my $collation = Text::Tradition::Collation->new(); |
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50 | my $stemma = Text::Tradition::Stemma->new( 'collation' => $collation, 'dot' => $dotfile ); |
51 | unlink( $dotfile ) if $must_unlink; |
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52 | $c->stash->{result} = $stemma->as_svg; |
53 | $c->forward( "View::SVG" ); |
54 | } |
55 | |
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56 | =head2 character_matrix |
57 | |
58 | Given an alignment table in JSON form, in the parameter 'alignment', returns a |
59 | character matrix suitable for input to Phylip PARS. |
60 | |
61 | =cut |
62 | |
63 | sub character_matrix :Local { |
64 | my( $self, $c ) = @_; |
65 | my $json = $c->request->params->{'alignment'}; |
66 | $c->log->debug( $json ); |
67 | my $table = from_json( $json ); |
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68 | my $matrix = character_input( $table ); |
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69 | $c->stash->{'result'} = { 'matrix' => $matrix }; |
70 | $c->forward( 'View::JSON' ); |
71 | } |
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72 | |
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73 | =head2 run_pars |
74 | |
75 | Takes either an alignment table in JSON format (passed as the parameter 'alignment') |
76 | or a character matrix Phylip accepts (passed as the parameter 'matrix'). Returns |
77 | either the Newick-format answer or an SVG representation of the graph. |
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78 | |
79 | =cut |
80 | |
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81 | sub run_pars :Local { |
82 | my( $self, $c ) = @_; |
83 | my $error; |
84 | my $view = 'View::JSON'; |
85 | my $matrix; |
86 | if( $c->request->param('matrix') ) { |
87 | $matrix = $c->request->param('matrix'); |
88 | } elsif( $c->request->param('alignment') ) { |
89 | # Make the matrix from the alignment |
90 | my $table = from_json( $c->request->param('alignment') ); |
91 | $matrix = character_input( $table ); |
92 | } else { |
93 | $error = "Must pass either an alignment or a matrix"; |
94 | } |
95 | |
96 | # Got the matrix, so try to run pars. |
97 | my( $result, $output ); |
98 | unless( $error ) { |
99 | ( $result, $output ) = phylip_pars( $matrix ); |
100 | $error = $output unless( $result ); |
101 | } |
102 | |
103 | # Did we want newick or a graph? |
104 | unless( $error ) { |
105 | my $format = 'newick'; |
106 | $format = $c->request->param('format') if $c->request->param('format'); |
107 | if( $format eq 'svg' ) { |
108 | # Do something |
109 | $c->stash->{'result'} = newick_to_svg( $output ); |
110 | $view = 'View::SVG'; |
111 | } elsif( $format ne 'newick' ) { |
112 | $error = "Requested output format $format unknown"; |
113 | } else { |
114 | $c->stash->{'result'} = { 'tree' => $output }; |
115 | } |
116 | } |
117 | |
118 | if( $error ) { |
119 | $c->stash->{'error'} = $error; |
120 | } # else the stash is populated. |
121 | $c->forward( $view ); |
122 | } |
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123 | |
124 | =head1 AUTHOR |
125 | |
126 | Tara L Andrews |
127 | |
128 | =head1 LICENSE |
129 | |
130 | This library is free software. You can redistribute it and/or modify |
131 | it under the same terms as Perl itself. |
132 | |
133 | =cut |
134 | |
135 | __PACKAGE__->meta->make_immutable; |
136 | |
137 | 1; |