biblicit 2.0.3 → 2.0.4
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- data/README.md +0 -2
- data/biblicit.gemspec +1 -1
- data/parscit/bin/citeExtract.pl +9 -161
- data/parscit/bin/sectExtract.pl +0 -14
- data/parscit/lib/ParsCit/Controller.pm +0 -59
- data/parscit/lib/ParsCit/PreProcess.pm +0 -4
- data/parscit/lib/ParsCit/Tr2crfpp.pm +1 -7
- metadata +4 -24
- data/parscit/bin/sectLabel/processOmniXML.pl +0 -1427
- data/parscit/bin/sectLabel/processOmniXML_new.pl +0 -1025
- data/parscit/bin/sectLabel/processOmniXMLv2.pl +0 -1529
- data/parscit/bin/sectLabel/processOmniXMLv3.pl +0 -964
- data/parscit/bin/sectLabel/simplifyOmniXML.pl +0 -382
- data/parscit/bin/xml2train.pl +0 -193
- data/parscit/lib/Omni/Config.pm +0 -93
- data/parscit/lib/Omni/Omnicell.pm +0 -263
- data/parscit/lib/Omni/Omnicol.pm +0 -292
- data/parscit/lib/Omni/Omnidd.pm +0 -328
- data/parscit/lib/Omni/Omnidoc.pm +0 -153
- data/parscit/lib/Omni/Omniframe.pm +0 -223
- data/parscit/lib/Omni/Omniline.pm +0 -423
- data/parscit/lib/Omni/Omnipage.pm +0 -282
- data/parscit/lib/Omni/Omnipara.pm +0 -232
- data/parscit/lib/Omni/Omnirun.pm +0 -303
- data/parscit/lib/Omni/Omnitable.pm +0 -336
- data/parscit/lib/Omni/Omniword.pm +0 -162
- data/parscit/lib/Omni/Traversal.pm +0 -313
- data/parscit/lib/SectLabel/AAMatching.pm +0 -1949
@@ -1,263 +0,0 @@
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package Omni::Omnicell;
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# Configuration
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use strict;
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# Local libraries
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use Omni::Config;
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use Omni::Omnipara;
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# Extern libraries
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use XML::Twig;
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use XML::Parser;
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# Global variables
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my $tag_list = $Omni::Config::tag_list;
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my $att_list = $Omni::Config::att_list;
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my $obj_list = $Omni::Config::obj_list;
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# Temporary variables
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my $tmp_content = undef;
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my $tmp_alignment = undef;
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my $tmp_grid_col_from = undef;
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my $tmp_grid_col_to = undef;
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my $tmp_grid_row_from = undef;
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my $tmp_grid_row_to = undef;
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my $tmp_vertical_align = undef;
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# My observation is that <table> contains <gridTable> and <cell>
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# <gridTable> contain the base grid's coordinates
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# <cell> contain the cell's position based on <gridTable> coordinates
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# and various types of objects: <picture>, <para>, may be even <dd> but
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# I'm not quite sure about this
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my @tmp_objs = ();
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###
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# A cell object in Omnipage xml: a cell is an essential member of <table> object
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#
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# Do Hoang Nhat Huy, 14 Feb 2011
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###
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# Initialization
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sub new
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{
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my ($class) = @_;
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# Objs: a paragraph can have many cells
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my @objs = ();
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# Class members
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my $self = { '_self' => $obj_list->{ 'OMNICELL' },
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'_raw' => undef,
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'_content' => undef,
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'_alignment' => undef,
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'_row_from' => undef,
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'_row_to' => undef,
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'_col_from' => undef,
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'_col_to' => undef,
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'_v_alignment' => undef,
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'_objs' => \@objs };
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bless $self, $class;
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return $self;
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}
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#
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sub set_raw
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{
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my ($self, $raw) = @_;
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# Save the raw xml <cell> ... </cell>
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$self->{ '_raw' } = $raw;
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# Parse the raw string
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my $twig_roots = { $tag_list->{ 'CELL' } => 1 };
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my $twig_handlers = { $tag_list->{ 'CELL' } => \&parse};
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# XML::Twig
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my $twig = new XML::Twig( twig_roots => $twig_roots,
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twig_handlers => $twig_handlers,
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pretty_print => 'indented' );
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# Start the XML parsing
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$twig->parse($raw);
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$twig->purge;
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# Copy information from temporary variables to class members
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$self->{ '_alignment' } = $tmp_alignment;
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$self->{ '_row_from' } = $tmp_grid_row_from;
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$self->{ '_row_to' } = $tmp_grid_row_to;
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$self->{ '_col_from' } = $tmp_grid_col_from;
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$self->{ '_col_to' } = $tmp_grid_col_to;
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$self->{ '_v_alignment' } = $tmp_vertical_align;
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# Copy all objects
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@{$self->{ '_objs' } } = @tmp_objs;
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# Copy content
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$self->{ '_content' } = $tmp_content;
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}
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sub get_raw
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{
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my ($self) = @_;
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return $self->{ '_raw' };
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}
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sub parse
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{
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my ($twig, $node) = @_;
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# At first, content is blank
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$tmp_content = "";
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# because there's no line
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@tmp_objs = ();
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# Get <cell> node attributes
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$tmp_alignment = GetNodeAttr($node, $att_list->{ 'ALIGN' });
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$tmp_grid_row_from = GetNodeAttr($node, $att_list->{ 'GROWFROM' });
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$tmp_grid_row_to = GetNodeAttr($node, $att_list->{ 'GROWTO' });
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$tmp_grid_col_from = GetNodeAttr($node, $att_list->{ 'GCOLFROM' });
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$tmp_grid_col_to = GetNodeAttr($node, $att_list->{ 'GCOLTO' });
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# TODO: don't understand, attribute with value = 0 will be returned as undef by twig
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$tmp_grid_row_from = ($tmp_grid_row_from ne "") ? $tmp_grid_row_from : 0;
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$tmp_grid_row_to = ($tmp_grid_row_to ne "") ? $tmp_grid_row_to : 0;
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$tmp_grid_col_from = ($tmp_grid_col_from ne "") ? $tmp_grid_col_from : 0;
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$tmp_grid_col_to = ($tmp_grid_col_to ne "") ? $tmp_grid_col_to : 0;
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$tmp_vertical_align = GetNodeAttr($node, $att_list->{ 'VALIGN' });
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# Check if there's any object: <para> and <picture object: <para> and <picture>
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my $img_tag = $tag_list->{ 'PICTURE' };
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my $para_tag = $tag_list->{ 'PARA' };
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my $child = undef;
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# Get the first child in the body text
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$child = $node->first_child();
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while (defined $child)
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{
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my $xpath = $child->path();
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# if this child is a <para> tag
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if ($xpath =~ m/\/$para_tag$/)
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{
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my $para = new Omni::Omnipara();
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# Set raw content
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$para->set_raw($child->sprint());
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# Update paragraph list
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push @tmp_objs, $para;
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# Update content
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$tmp_content = $tmp_content . $para->get_content() . "\n";
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}
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# if this child is a <picture> tag
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elsif ($xpath =~ m/\/$img_tag$/)
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{
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#my $img = new Omni::Omniimg();
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# Set raw content
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#$img->set_raw($child->sprint());
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# Update paragraph list
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#push @tmp_objs, $img;
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# Update content
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#$tmp_content = $tmp_content . $img->get_content() . "\n";
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}
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# Little brother
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if ($child->is_last_child)
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{
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last;
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}
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else
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{
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$child = $child->next_sibling();
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}
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}
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}
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sub get_name
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{
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my ($self) = @_;
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return $self->{ '_self' };
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}
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sub get_objs_ref
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{
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my ($self) = @_;
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return $self->{ '_objs' };
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}
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sub get_content
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{
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my ($self) = @_;
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return $self->{ '_content' };
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}
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sub get_alignment
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{
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my ($self) = @_;
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return $self->{ '_alignment' };
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}
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sub get_grid_row_from
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{
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my ($self) = @_;
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return $self->{ '_row_from' };
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}
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sub get_grid_row_to
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{
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my ($self) = @_;
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return $self->{ '_row_to' };
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}
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sub get_grid_col_from
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{
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my ($self) = @_;
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return $self->{ '_col_from' };
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}
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sub get_grid_col_to
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{
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my ($self) = @_;
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return $self->{ '_col_to' };
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}
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sub get_vertical_alignment
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{
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my ($self) = @_;
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return $self->{ '_v_alignment' };
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}
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# Support functions
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sub GetNodeAttr
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{
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my ($node, $attr) = @_;
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return ($node->att($attr) ? $node->att($attr) : "");
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}
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sub SetNodeAttr
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{
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my ($node, $attr, $value) = @_;
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$node->set_att($attr, $value);
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}
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sub GetNodeText
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{
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my ($node) = @_;
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return $node->text;
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}
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sub SetNodeText
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{
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my ($node, $value) = @_;
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$node->set_text($value);
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}
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1;
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data/parscit/lib/Omni/Omnicol.pm
DELETED
@@ -1,292 +0,0 @@
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package Omni::Omnicol;
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# Configuration
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use strict;
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# Local libraries
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use Omni::Config;
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use Omni::Omnidd;
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use Omni::Omnipara;
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use Omni::Omniframe;
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use Omni::Omnitable;
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# Extern libraries
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use XML::Twig;
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use XML::Parser;
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# Global variables
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my $tag_list = $Omni::Config::tag_list;
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my $att_list = $Omni::Config::att_list;
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my $obj_list = $Omni::Config::obj_list;
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# Temporary variables
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###
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# A column object in Omnipage xml: a column contains zero or many paragraphs
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#
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# Do Hoang Nhat Huy, 11 Jan 2011
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###
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# Initialization
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sub new
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{
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my ($class) = @_;
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# Column: a column can have many paragraphs, dd, tables, or pictures
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my @objs = ();
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# Class members
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my $self = { '_self' => $obj_list->{ 'OMNICOL' },
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'_raw' => undef,
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'_content' => undef,
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'_bottom' => undef,
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'_top' => undef,
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'_left' => undef,
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'_right' => undef,
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'_objs' => \@objs };
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bless $self, $class;
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return $self;
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}
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#
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sub set_raw
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{
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my ($self, $raw) = @_;
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# Save the raw xml <column> ... </column>
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$self->{ '_raw' } = $raw;
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# Parse the raw string
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my $twig_roots = { $tag_list->{ 'COLUMN' } => 1 };
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my $twig_handlers = { $tag_list->{ 'COLUMN' } => sub { parse(@_, \$self); } };
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# XML::Twig
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my $twig = new XML::Twig( twig_roots => $twig_roots,
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twig_handlers => $twig_handlers,
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pretty_print => 'indented' );
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# Start the XML parsing
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$twig->parse($raw, \$self);
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$twig->purge;
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}
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sub get_raw
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{
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my ($self) = @_;
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return $self->{ '_raw' };
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}
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sub parse
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{
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my ($twig, $node, $self) = @_;
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# At first, content is blank
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my $tmp_content = "";
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# because there's no object
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my @tmp_objs = ();
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# Get <column> node attributes
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my $tmp_bottom = GetNodeAttr($node, $att_list->{ 'BOTTOM' });
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my $tmp_top = GetNodeAttr($node, $att_list->{ 'TOP' });
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my $tmp_left = GetNodeAttr($node, $att_list->{ 'LEFT' });
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my $tmp_right = GetNodeAttr($node, $att_list->{ 'RIGHT' });
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# Check if there's any paragraph, dd, table, or picture
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# The large number of possible children is due to the
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# ambiguous structure of the Omnipage XML
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my $dd_tag = $tag_list->{ 'DD' };
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my $img_tag = $tag_list->{ 'PICTURE' };
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my $para_tag = $tag_list->{ 'PARA' };
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my $table_tag = $tag_list->{ 'TABLE' };
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my $column_tag = $tag_list->{ 'COLUMN' };
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102
|
-
my $frame_tag = $tag_list->{ 'FRAME' };
|
103
|
-
|
104
|
-
my $child = undef;
|
105
|
-
# Get the first child in the body text
|
106
|
-
$child = $node->first_child();
|
107
|
-
|
108
|
-
while (defined $child)
|
109
|
-
{
|
110
|
-
my $xpath = $child->path();
|
111
|
-
|
112
|
-
# if this child is a <para> tag
|
113
|
-
if ($xpath =~ m/\/$para_tag$/)
|
114
|
-
{
|
115
|
-
my $para = new Omni::Omnipara();
|
116
|
-
|
117
|
-
# Set raw content
|
118
|
-
$para->set_raw($child->sprint());
|
119
|
-
|
120
|
-
# Update paragraph list
|
121
|
-
push @tmp_objs, $para;
|
122
|
-
|
123
|
-
# Update content
|
124
|
-
$tmp_content = $tmp_content . $para->get_content() . "\n";
|
125
|
-
}
|
126
|
-
# TODO: I'll handle this one later. Seriously
|
127
|
-
# if this child is a <dd> tag
|
128
|
-
elsif ($xpath =~ m/\/$dd_tag$/)
|
129
|
-
{
|
130
|
-
#my $dd = new Omni::Omnidd();
|
131
|
-
|
132
|
-
# Set raw content
|
133
|
-
#$dd->set_raw($child->sprint());
|
134
|
-
|
135
|
-
# Update paragraph list
|
136
|
-
#push @tmp_objs, $dd;
|
137
|
-
|
138
|
-
# Update content
|
139
|
-
#$tmp_content = $tmp_content . $dd->get_content() . "\n";
|
140
|
-
}
|
141
|
-
# if this child is a <table> tag
|
142
|
-
elsif ($xpath =~ m/\/$table_tag$/)
|
143
|
-
{
|
144
|
-
my $table = new Omni::Omnitable();
|
145
|
-
|
146
|
-
# Set raw content
|
147
|
-
$table->set_raw($child->sprint());
|
148
|
-
|
149
|
-
# Update paragraph list
|
150
|
-
push @tmp_objs, $table;
|
151
|
-
|
152
|
-
# Update content
|
153
|
-
$tmp_content = $tmp_content . $table->get_content() . "\n";
|
154
|
-
}
|
155
|
-
# if this child is a <picture> tag
|
156
|
-
elsif ($xpath =~ m/\/$img_tag$/)
|
157
|
-
{
|
158
|
-
#my $img = new Omni::Omniimg();
|
159
|
-
|
160
|
-
# Set raw content
|
161
|
-
#$img->set_raw($child->sprint());
|
162
|
-
|
163
|
-
# Update paragraph list
|
164
|
-
#push @tmp_objs, $img;
|
165
|
-
|
166
|
-
# Update content
|
167
|
-
#$tmp_content = $tmp_content . $img->get_content() . "\n";
|
168
|
-
}
|
169
|
-
# if this child is a <column> tag
|
170
|
-
elsif ($xpath =~ m/\/$column_tag$/)
|
171
|
-
{
|
172
|
-
my $col = new Omni::Omnicol();
|
173
|
-
|
174
|
-
# Set raw content
|
175
|
-
$col->set_raw($child->sprint());
|
176
|
-
|
177
|
-
# Nested <column> is not allowed so we copy the objects
|
178
|
-
my $objects = $col->get_objs_ref();
|
179
|
-
|
180
|
-
# Update <column> objects list
|
181
|
-
push @tmp_objs, @{ $objects };
|
182
|
-
|
183
|
-
# Update content
|
184
|
-
$tmp_content = $tmp_content . $col->get_content() . "\n";
|
185
|
-
}
|
186
|
-
# if this child is <frame>
|
187
|
-
elsif ($xpath =~ m/\/$frame_tag$/)
|
188
|
-
{
|
189
|
-
my $frame = new Omni::Omniframe();
|
190
|
-
|
191
|
-
# Set raw content
|
192
|
-
$frame->set_raw($child->sprint());
|
193
|
-
|
194
|
-
# Update column list
|
195
|
-
push @tmp_objs, $frame;
|
196
|
-
|
197
|
-
# Update content
|
198
|
-
$tmp_content = $tmp_content . $frame->get_content() . "\n";
|
199
|
-
}
|
200
|
-
|
201
|
-
# Little brother
|
202
|
-
if ($child->is_last_child)
|
203
|
-
{
|
204
|
-
last;
|
205
|
-
}
|
206
|
-
else
|
207
|
-
{
|
208
|
-
$child = $child->next_sibling();
|
209
|
-
}
|
210
|
-
}
|
211
|
-
|
212
|
-
# Copy information from temporary variables to class members
|
213
|
-
$$self->{ '_bottom' } = $tmp_bottom;
|
214
|
-
$$self->{ '_top' } = $tmp_top;
|
215
|
-
$$self->{ '_left' } = $tmp_left;
|
216
|
-
$$self->{ '_right' } = $tmp_right;
|
217
|
-
|
218
|
-
# Copy all objects
|
219
|
-
@{$$self->{ '_objs' } } = @tmp_objs;
|
220
|
-
|
221
|
-
# Copy content
|
222
|
-
$$self->{ '_content' } = $tmp_content;
|
223
|
-
}
|
224
|
-
|
225
|
-
sub get_name
|
226
|
-
{
|
227
|
-
my ($self) = @_;
|
228
|
-
return $self->{ '_self' };
|
229
|
-
}
|
230
|
-
|
231
|
-
sub get_objs_ref
|
232
|
-
{
|
233
|
-
my ($self) = @_;
|
234
|
-
return $self->{ '_objs' };
|
235
|
-
}
|
236
|
-
|
237
|
-
sub get_content
|
238
|
-
{
|
239
|
-
my ($self) = @_;
|
240
|
-
return $self->{ '_content' };
|
241
|
-
}
|
242
|
-
|
243
|
-
sub get_bottom_pos
|
244
|
-
{
|
245
|
-
my ($self) = @_;
|
246
|
-
return $self->{ '_bottom' };
|
247
|
-
}
|
248
|
-
|
249
|
-
sub get_top_pos
|
250
|
-
{
|
251
|
-
my ($self) = @_;
|
252
|
-
return $self->{ '_top' };
|
253
|
-
}
|
254
|
-
|
255
|
-
sub get_left_pos
|
256
|
-
{
|
257
|
-
my ($self) = @_;
|
258
|
-
return $self->{ '_left' };
|
259
|
-
}
|
260
|
-
|
261
|
-
sub get_right_pos
|
262
|
-
{
|
263
|
-
my ($self) = @_;
|
264
|
-
return $self->{ '_right' };
|
265
|
-
}
|
266
|
-
|
267
|
-
# Support functions
|
268
|
-
sub GetNodeAttr
|
269
|
-
{
|
270
|
-
my ($node, $attr) = @_;
|
271
|
-
return ($node->att($attr) ? $node->att($attr) : "");
|
272
|
-
}
|
273
|
-
|
274
|
-
sub SetNodeAttr
|
275
|
-
{
|
276
|
-
my ($node, $attr, $value) = @_;
|
277
|
-
$node->set_att($attr, $value);
|
278
|
-
}
|
279
|
-
|
280
|
-
sub GetNodeText
|
281
|
-
{
|
282
|
-
my ($node) = @_;
|
283
|
-
return $node->text;
|
284
|
-
}
|
285
|
-
|
286
|
-
sub SetNodeText
|
287
|
-
{
|
288
|
-
my ($node, $value) = @_;
|
289
|
-
$node->set_text($value);
|
290
|
-
}
|
291
|
-
|
292
|
-
1;
|