--- /dev/null
+package TreeOfTexts::Controller::Microservice;
+use Moose;
+use namespace::autoclean;
+use JSON;
+use Text::Tradition;
+use Text::Tradition::Stemma;
+use Text::Tradition::StemmaUtil qw/ character_input phylip_pars newick_to_svg /;
+
+BEGIN { extends 'Catalyst::Controller' }
+
+=head1 NAME
+
+TreeOfTexts::Controller::Microservice - Controller for TreeOfTexts standalone
+components
+
+=head1 DESCRIPTION
+
+This package contains the pieces of web functionality relating to text tradition
+objects that are useful outside the framework of this application.
+
+=head1 COLLATION PARSING INPUT
+
+Each URL call which operates on a provided collation is called by POST with the
+following form parameters in the body:
+
+=over 4
+
+=item * type - Can be one of CollateX, CSV, JSON, nCritic, TEI, Tabular.
+
+=item * data - The collation data itself.
+
+=back
+
+=head1 COLLATION URLs
+
+=head2 renderSVG
+
+ POST microservice/renderSVG
+
+Parse the passed collation data and return an SVG of the collated text.
+
+=cut
+
+# Utility function to render SVG from a collation in some recognized format.
+sub renderSVG :Local :Args(0) {
+ my( $self, $c ) = @_;
+ my $tradition = _parse_to_tradition( $c->request );
+ $c->stash->{'result'} = $tradition->collation->as_svg;
+ $c->forward('View::SVG');
+}
+
+=head1 STEMMA / DISTANCE TREE URLs
+
+=head2 stemma_svg
+
+ POST microservice/stemma_svg
+
+Parameter: dot => a string containing the dot description of the stemma.
+
+=cut
+
+sub stemma_svg :Local :Args(0) {
+ my( $self, $c ) = @_;
+ my $t = Text::Tradition->new();
+ my $stemma = $t->add_stemma( 'dot' => $c->req->param('dot') );
+ $c->stash->{'result'} = $stemma->as_svg;
+ $c->forward('View::SVG');
+}
+
+=head2 character_matrix
+
+ POST microservice/character_matrix
+
+Given an alignment table in JSON form, in the parameter 'alignment', returns a
+character matrix suitable for input to Phylip PARS.
+
+=cut
+
+sub character_matrix :Local :Args(0) {
+ my( $self, $c ) = @_;
+ my $json = $c->request->params->{'alignment'};
+ $c->log->debug( $json );
+ my $table = from_json( $json );
+ my $matrix = character_input( $table );
+ $c->stash->{'result'} = { 'matrix' => $matrix };
+ $c->forward( 'View::JSON' );
+}
+
+=head2 run_pars
+
+ POST microservice/run_pars
+
+Runs Phylip PARS on the provided alignment, and returns the result. Parameters include:
+
+=over 4
+
+=item * alignment - A JSON alignment table, as produced by CollateX
+
+=item * matrix - A character matrix suitable for Phylip.
+
+=item * format - The format in which to return the results. Default is 'newick'; also allowed is 'svg'.
+
+=back
+
+Exactly one of 'alignment' or 'matrix' must be specified.
+
+=cut
+
+sub run_pars :Local :Args(0) {
+ my( $self, $c ) = @_;
+ my $error;
+ my $view = 'View::JSON';
+ my $matrix;
+ if( $c->request->param('matrix') ) {
+ $matrix = $c->request->param('matrix');
+ } elsif( $c->request->param('alignment') ) {
+ # Make the matrix from the alignment
+ my $table = from_json( $c->request->param('alignment') );
+ $matrix = character_input( $table );
+ } else {
+ $error = "Must pass either an alignment or a matrix";
+ }
+
+ # Got the matrix, so try to run pars.
+ my( $result, $output );
+ unless( $error ) {
+ ( $result, $output ) = phylip_pars( $matrix );
+ $error = $output unless( $result );
+ }
+
+ # Did we want newick or a graph?
+ unless( $error ) {
+ my $format = 'newick';
+ $format = $c->request->param('format') if $c->request->param('format');
+ if( $format eq 'svg' ) {
+ # Do something
+ $c->stash->{'result'} = newick_to_svg( $output );
+ $view = 'View::SVG';
+ } elsif( $format ne 'newick' ) {
+ $error = "Requested output format $format unknown";
+ } else {
+ $c->stash->{'result'} = { 'tree' => $output };
+ }
+ }
+
+ if( $error ) {
+ $c->stash->{'error'} = $error;
+ } # else the stash is populated.
+ $c->forward( $view );
+}
+
+
+=head1 OPENSOCIAL URLs
+
+=head2 view_table
+
+Simple gadget to return the analysis table for the stexaminer
+
+=cut
+
+sub view_table :Local :Args(0) {
+ my( $self, $c ) = @_;
+ my $m = $c->model('Directory');
+ my $id = $c->request->params->{'textid'};
+ my $t = run_analysis( $m->tradition( $id ), $m->stemma( $id ) );
+ $c->stash->{variants} = $t->{'variants'};
+ $c->stash->{template} = 'table_gadget.tt';
+}
+
+=head2 view_stemma_svg
+
+Simple gadget to return the SVG for a given stemma
+
+=cut
+
+sub view_svg :Local :Args(0) {
+ my( $self, $c ) = @_;
+ my $m = $c->model('Directory');
+ my $stemma = $m->tradition( $c->request->params->{'textid'} )->stemma;
+ if( $stemma ) {
+ $c->stash->{svg} = $stemma->as_svg;
+ }
+ $c->stash->{template} = 'stemma_gadget.tt';
+}
+
+=head2 default
+
+Standard 404 error page
+
+=cut
+
+sub default :Path {
+ my ( $self, $c ) = @_;
+ $c->response->body( 'Page not found' );
+ $c->response->status(404);
+}
+
+## Internal utility function
+
+sub _parse_to_tradition {
+ my $req = shift;
+ my $type = $req->body_params->{'type'};
+ my $name = $req->param('name') || 'Collation graph';
+ my $data = $req->body_params->{'data'};
+ my $opts = {
+ 'name' => $name,
+ 'input' => $type,
+ 'string' => $data
+ };
+ $opts->{'sep_char'} = ',' if $type eq 'CSV';
+ $opts->{'sep_char'} = "\t" if $type eq 'TabSep';
+ return Text::Tradition->new( $opts );
+}
+
+=head2 end
+
+Attempt to render a view, if needed.
+
+=cut
+
+sub end : ActionClass('RenderView') {}
+
+=head1 AUTHOR
+
+Tara L Andrews
+
+=head1 LICENSE
+
+This library is free software. You can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+__PACKAGE__->meta->make_immutable;
+
+1;
--- /dev/null
+package TreeOfTexts::Controller::Relation;
+use Moose;
+use namespace::autoclean;
+
+BEGIN { extends 'Catalyst::Controller' }
+
+
+=head1 NAME
+
+TreeOfTexts::Controller::Relation - Controller for the relationship mapper
+
+=head1 DESCRIPTION
+
+The stemma analysis tool with the pretty colored table.
+
+=head1 METHODS
+
+ GET relation/$textid
+
+Renders the application for the text identified by $textid.
+
+=head2 index
+
+The relationship editor tool.
+
+=cut
+
+sub index :Path :Args(1) {
+ my( $self, $c, $textid ) = @_;
+ my $m = $c->model('Directory');
+ my $tradition = $m->tradition( $textid );
+ my $table = $tradition->collation->make_alignment_table();
+ my $witlist = map { $_->{'witness'} } @{$table->{'alignment'}};
+ $c->stash->{witnesses} = $witlist;
+ $c->stash->{alignment} = $table;
+ $c->stash->{template} = 'relate.tt';
+}
+
+=head2 end
+
+Attempt to render a view, if needed.
+
+=cut
+
+sub end : ActionClass('RenderView') {}
+
+=head1 AUTHOR
+
+Tara L Andrews
+
+=head1 LICENSE
+
+This library is free software. You can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+__PACKAGE__->meta->make_immutable;
+
+1;
Serves a snippet of HTML that lists the available texts. Eventually this will be available texts by user.
=cut
-sub directory :Path :Args(0) {
+sub directory :Local :Args(0) {
my( $self, $c ) = @_;
my $m = $c->model('Directory');
# TODO not used yet, will load user texts later
'id' => $id,
'name' => $m->name( $id ),
};
- push( @all_texts, $data );
+ push( @textlist, $data );
}
$c->stash->{texts} = \@textlist;
=cut
-sub alignment :Path :Args(1) {
+sub alignment :Local :Args(1) {
my( $self, $c, $textid ) = @_;
my $m = $c->model('Directory');
my $collation = $m->tradition( $textid )->collation;
=cut
-sub stemma :Path :Args(1) {
+sub stemma :Local :Args(1) {
my( $self, $c, $textid ) = @_;
my $m = $c->model('Directory');
my $tradition = $m->tradition( $textid );
=cut
-sub stemma :Path :Args(1) {
+sub stemmadot :Local :Args(1) {
my( $self, $c, $textid ) = @_;
my $m = $c->model('Directory');
my $tradition = $m->tradition( $textid );
$c->forward('View::Plain');
}
-=head2 relationships
-
-The relationship editor tool.
-
-=cut
-
-sub relationships :Local {
- my( $self, $c ) = @_;
- my $m = $c->model('Directory');
- my $tradition = $m->tradition( $c->request->params->{'textid'} );
- my $table = $tradition->collation->make_alignment_table();
- my $witlist = map { $_->{'witness'} } @{$table->{'alignment'}};
- $c->stash->{witnesses} = $witlist;
- $c->stash->{alignment} = $table;
- $c->stash->{template} = 'relate.tt';
-}
-
-=head2 stexaminer
-
-The stemma analysis tool with the pretty colored table.
-
-=cut
-
-sub stexaminer :Local {
- my( $self, $c ) = @_;
- my $m = $c->model('Directory');
- my $tradition = $m->tradition( $c->request->params->{'textid'} );
- my $stemma = $tradition->stemma;
- # TODO Think about caching the stemma in a session
- $c->stash->{svg} = $stemma->as_svg;
- $c->stash->{text_title} = $tradition->name;
- $c->stash->{template} = 'index.tt';
- # TODO Run the analysis as AJAX from the loaded page.
- my $t = run_analysis( $tradition );
- $c->stash->{variants} = $t->{'variants'};
- $c->stash->{total} = $t->{'variant_count'};
- $c->stash->{genealogical} = $t->{'genealogical_count'};
- $c->stash->{conflict} = $t->{'conflict_count'};
-}
-
-=head1 MICROSERVICE CALLS
-
-=head2 renderSVG
-
-Parse the passed collation data and return an SVG of the collated text. Takes
-the following parameters:
-
-=over 4
-
-=item * data - The collation data itself.
-
-=item * input - The data format. Valid values include CollateX, Self, TEI (for parallel segmentation) eventually Tabular.
-
-=item * name - A name for the text. Not so important for this function.
-
-=cut
-
-# Utility function to render SVG from a graph input.
-sub renderSVG :Local {
- my( $self, $c ) = @_;
- my $format = $c->request->param('format') || 'string';
- my $type = $c->request->body_params->{'type'};
- my $name = $c->request->param('name') || 'Collation graph';
- my $data = $c->request->body_params->{'data'};
- $c->log->debug( $data );
- my $tradition = Text::Tradition->new(
- 'name' => $name,
- 'input' => $type,
- $format => $data,
- );
- $c->log->debug( "Got tradition with " . $tradition->collation->readings . " readings" );
- $c->stash->{'result'} = $tradition->collation->as_svg;
- $c->forward('View::SVG');
-}
-
-
-=head1 OPENSOCIAL URLs
-
-=head2 view_table
-
-Simple gadget to return the analysis table for the stexaminer
-
-=cut
-
-sub view_table :Local {
- my( $self, $c ) = @_;
- my $m = $c->model('Directory');
- my $id = $c->request->params->{'textid'};
- my $t = run_analysis( $m->tradition( $id ), $m->stemma( $id ) );
- $c->stash->{variants} = $t->{'variants'};
- $c->stash->{template} = 'table_gadget.tt';
-}
-
-=head2 view_svg
-
-Simple gadget to return the SVG for a given stemma
-
-=cut
-
-sub view_svg :Local {
- my( $self, $c ) = @_;
- my $m = $c->model('Directory');
- my $stemma = $m->tradition( $c->request->params->{'textid'} )->stemma;
- if( $stemma ) {
- $c->stash->{svg} = $stemma->as_svg;
- }
- $c->stash->{template} = 'stemma_gadget.tt';
-}
-
=head2 default
Standard 404 error page
+++ /dev/null
-package TreeOfTexts::Controller::Stemmagraph;
-use Moose;
-use namespace::autoclean;
-use File::Temp;
-use JSON;
-use Text::Tradition::Collation;
-use Text::Tradition::StemmaUtil qw/ character_input phylip_pars newick_to_svg /;
-
-BEGIN { extends 'Catalyst::Controller' }
-
-#
-# Sets the actions in this controller to be registered with no prefix
-# so they function identically to actions created in MyApp.pm
-#
-__PACKAGE__->config(namespace => '');
-
-=head1 NAME
-
-TreeOfTexts::Controller::Stemmagraph - Simple controller for stemma display
-
-=head1 DESCRIPTION
-
-[enter your description here]
-
-=head1 METHODS
-
-=cut
-
-sub get_graph :Local {
- my( $self, $c ) = @_;
- # If called interactively, we have params 'display', 'output', 'witnesses'
- # If called non-interactively, we look at headers and content.
- # The body is actually a File::Temp object; this is undocumented but
- # so it seems to be.
- my $dotfile;
- my $must_unlink = 0;
- if( $c->request->params->{'dot'} ) {
- # Make a File::Temp object.
- my $tmpfile = File::Temp->new( UNLINK => 0 );
- print $tmpfile $c->request->params->{'dot'};
- $dotfile = $tmpfile->filename;
- $must_unlink = 1;
- } else {
- $dotfile = $c->request->body;
- }
- my $format = 'svg';
-
- # Render the dot in the given format.
- my $collation = Text::Tradition::Collation->new();
- my $stemma = Text::Tradition::Stemma->new( 'collation' => $collation, 'dot' => $dotfile );
- unlink( $dotfile ) if $must_unlink;
- $c->stash->{result} = $stemma->as_svg;
- $c->forward( "View::SVG" );
-}
-
-=head2 character_matrix
-
-Given an alignment table in JSON form, in the parameter 'alignment', returns a
-character matrix suitable for input to Phylip PARS.
-
-=cut
-
-sub character_matrix :Local {
- my( $self, $c ) = @_;
- my $json = $c->request->params->{'alignment'};
- $c->log->debug( $json );
- my $table = from_json( $json );
- my $matrix = character_input( $table );
- $c->stash->{'result'} = { 'matrix' => $matrix };
- $c->forward( 'View::JSON' );
-}
-
-=head2 run_pars
-
-Takes either an alignment table in JSON format (passed as the parameter 'alignment')
-or a character matrix Phylip accepts (passed as the parameter 'matrix'). Returns
-either the Newick-format answer or an SVG representation of the graph.
-
-=cut
-
-sub run_pars :Local {
- my( $self, $c ) = @_;
- my $error;
- my $view = 'View::JSON';
- my $matrix;
- if( $c->request->param('matrix') ) {
- $matrix = $c->request->param('matrix');
- } elsif( $c->request->param('alignment') ) {
- # Make the matrix from the alignment
- my $table = from_json( $c->request->param('alignment') );
- $matrix = character_input( $table );
- } else {
- $error = "Must pass either an alignment or a matrix";
- }
-
- # Got the matrix, so try to run pars.
- my( $result, $output );
- unless( $error ) {
- ( $result, $output ) = phylip_pars( $matrix );
- $error = $output unless( $result );
- }
-
- # Did we want newick or a graph?
- unless( $error ) {
- my $format = 'newick';
- $format = $c->request->param('format') if $c->request->param('format');
- if( $format eq 'svg' ) {
- # Do something
- $c->stash->{'result'} = newick_to_svg( $output );
- $view = 'View::SVG';
- } elsif( $format ne 'newick' ) {
- $error = "Requested output format $format unknown";
- } else {
- $c->stash->{'result'} = { 'tree' => $output };
- }
- }
-
- if( $error ) {
- $c->stash->{'error'} = $error;
- } # else the stash is populated.
- $c->forward( $view );
-}
-
-=head1 AUTHOR
-
-Tara L Andrews
-
-=head1 LICENSE
-
-This library is free software. You can redistribute it and/or modify
-it under the same terms as Perl itself.
-
-=cut
-
-__PACKAGE__->meta->make_immutable;
-
-1;
--- /dev/null
+package TreeOfTexts::Controller::Stexaminer;
+use Moose;
+use namespace::autoclean;
+use File::Temp;
+use JSON;
+use Text::Tradition::Analysis qw/ run_analysis /;
+
+BEGIN { extends 'Catalyst::Controller' }
+
+
+=head1 NAME
+
+TreeOfTexts::Controller::Stexaminer - Simple controller for stemma display
+
+=head1 DESCRIPTION
+
+The stemma analysis tool with the pretty colored table.
+
+=head1 METHODS
+
+ GET stexaminer/$textid
+
+Renders the application for the text identified by $textid.
+
+=head2 index
+
+=cut
+
+sub index :Path :Args(1) {
+ my( $self, $c, $textid ) = @_;
+ my $m = $c->model('Directory');
+ my $tradition = $m->tradition( $textid );
+ my $stemma = $tradition->stemma;
+ # TODO Think about caching the stemma in a session
+ $c->stash->{svg} = $stemma->as_svg;
+ $c->stash->{text_title} = $tradition->name;
+ $c->stash->{template} = 'stexaminer.tt';
+ # TODO Run the analysis as AJAX from the loaded page.
+ my $t = run_analysis( $tradition );
+ $c->stash->{variants} = $t->{'variants'};
+ $c->stash->{total} = $t->{'variant_count'};
+ $c->stash->{genealogical} = $t->{'genealogical_count'};
+ $c->stash->{conflict} = $t->{'conflict_count'};
+}
+
+=head2 end
+
+Attempt to render a view, if needed.
+
+=cut
+
+sub end : ActionClass('RenderView') {}
+
+=head1 AUTHOR
+
+Tara L Andrews
+
+=head1 LICENSE
+
+This library is free software. You can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+__PACKAGE__->meta->make_immutable;
+
+1;
use strict;
use base 'Catalyst::View::Download::Plain';
+
+=head1 NAME
+
+TreeOfTexts::View::Plain - Catalyst view for plaintext files
+
+=head1 SYNOPSIS
+
+See L<TreeOfTexts>
+
+=head1 DESCRIPTION
+
+Catalyst plaintext View.
+
+=head1 AUTHOR
+
+Tara Andrews
+
+=head1 LICENSE
+
+This library is free software, you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+1;
projects / scpubgit/stemmatology.git / commitdiff