This file is indexed.

/usr/share/perl5/GO/Handlers/obj.pm is in libgo-perl 0.13-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
# $Id: obj.pm,v 1.24 2008/01/17 20:08:14 cmungall Exp $
#
# This GO module is maintained by Chris Mungall <cjm@fruitfly.org>
#
# see also - http://www.geneontology.org
#          - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself

=head1 NAME

  GO::Handlers::obj     - parses GO files into GO object model

=head1 SYNOPSIS

  use GO::Handlers::obj

=cut

=head1 DESCRIPTION

=head1 PUBLIC METHODS

=cut

# makes objects from parser events

package GO::Handlers::obj;
use Data::Stag qw(:all);
use GO::Parsers::ParserEventNames;
use base qw(GO::Handlers::base);
use strict qw(vars refs);

my $TRACE = $ENV{GO_TRACE};

sub init {
    my $self = shift;
    $self->SUPER::init;

    use GO::ObjCache;
    my $apph = GO::ObjCache->new;
    $self->{apph} = $apph;

    use GO::Model::Graph;
    my $g = $self->apph->create_graph_obj;
    $self->{g} = $g;
    return;
}


=head2 graph

  Usage   - my $terms = $obj_handler->graph->get_all_terms;
  Synonym - g
  Synonym - ontology
  Returns - GO::Model::Graph object
  Args    -

as files are parsed, objects are created; depending on what kind of
datatype is being parsed, the classes of the created objects will be
different - eg GO::Model::Term, GO::Model::Association etc

the way to access all of thses is through the top level graph object

eg

  $parser = GO::Parser->new({handler=>'obj'});
  $parser->parse(@files);
  my $graph = $parser->graph;
  

=cut

sub g {
    my $self = shift;
    $self->{g} = shift if @_;
    return $self->{g};
}

*graph = \&g;
*ontology = \&g;


sub apph {
    my $self = shift;
    $self->{apph} = shift if @_;
    return $self->{apph};
}

sub root_term {
    my $self = shift;
    $self->{_root_term} = shift if @_;
    return $self->{_root_term};
}

# 20041029 - not currently used
sub add_root {
    my $self = shift;
    my $g = $self->g;

    my $root = $self->apph->create_term_obj;
    $root->name('root');
    $root->acc('root');
    $g->add_term($root);
    $self->root_term($root);
    $self->root_to_be_added(1);
    $root;
}

# -- HANDLER METHODS --

sub e_obo {
    my $self = shift;
    my $g = $self->g;
    return ();
}

sub e_typedef {
    my $self = shift;
    my $t = shift;
    $self->stanza('Typedef', $t);
}

sub e_term {
    my $self = shift;
    my $t = shift;
    $self->stanza('Term', $t);
}

sub e_instance {
    my $self = shift;
    my $t = shift;
    $self->stanza('Instance', $t);
}

sub stanza {
    my $self = shift;
    my $stanza = lc(shift);
    my $tree = shift;
    my $acc = stag_get($tree, ID);
    if (!$acc) {
        $self->throw( "NO ACC: $@\n" );
    }
    my $term;
    eval {
        $term = $self->g->get_term($acc);
    };
    if ($@) {
        $self->throw( "ARG:$@" );
    }
    # no point adding term twice; we
    # assume the details are the same
    return $term if $term && $self->strictorder;

    $term = $self->apph->create_term_obj;

    if ($stanza eq 'typedef') {
        $term->is_relationship_type(1);
    }
    if ($stanza eq 'instance') {
        $term->is_instance(1);
    }

    my %h = ();
    foreach my $sn (stag_kids($tree)) {
        my $k = $sn->name;
        my $v = $sn->data;

        if ($k eq RELATIONSHIP) {
            my $obj = stag_get($sn, TO);
            $self->g->add_relationship($obj, $term->acc, stag_get($sn, TYPE));
        }
        elsif ($k eq IS_A) {
            $self->g->add_relationship($v, $term->acc, IS_A);
        }
        elsif ($k eq INSTANCE_OF) {
            $self->g->add_relationship($v, $term->acc, INSTANCE_OF);
        }
        elsif ($k eq DEF) {
            my $defstr = stag_get($sn, DEFSTR);
	    my @xrefs = stag_get($sn, DBXREF);
	    $term->definition($defstr);
	    $term->add_definition_dbxref($self->dbxref($_)) foreach @xrefs;
        }
        elsif ($k eq SYNONYM) {
            my $synstr = stag_get($sn, SYNONYM_TEXT);
            my $type = stag_find($sn, 'scope');
	    my @xrefs = stag_get($sn, DBXREF);
	    $term->add_synonym_by_type($type ? lc($type) : '', $synstr);
#	    $term->add_definition_dbxref($_) foreach @xrefs;
        }
        elsif ($k eq ALT_ID) {
	    $term->add_alt_id($v);
        }
        elsif ($k eq CONSIDER) {
	    $term->add_consider($v);
        }
        elsif ($k eq REPLACED_BY) {
	    $term->add_replaced_by($v);
        }
        elsif ($k eq ALT_ID) {
	    $term->add_alt_id($v);
        }
        elsif ($k eq XREF_ANALOG || $k eq XREF) {
            my $xref =
	      $self->apph->create_xref_obj(stag_pairs($sn));
            $term->add_dbxref($xref);
        }
        elsif ($k eq XREF_UNKNOWN) {
            my $xref =
	      $self->apph->create_xref_obj(stag_pairs($sn));
            $term->add_dbxref($xref);
        }
        elsif ($k eq ID) {
            $term->acc($v);
        }
        elsif ($k eq NAMESPACE) {
            $term->namespace($v);
        }
        elsif ($k eq NAME) {
            $term->name($v);
        }
        elsif ($k eq SUBSET) {
            $term->add_subset($v);
        }
        elsif ($k eq COMMENT) {
            $term->comment($v);
        }
        elsif ($k eq IS_ROOT) {
            $term->is_root($v);
        }
        elsif ($k eq BUILTIN) {
            # ignore
        }
        elsif ($k eq PROPERTY_VALUE) {
            # ignore
        }
        elsif ($k eq IS_METADATA_TAG) {
            # ignore
        }
        elsif ($k eq IS_OBSOLETE) {
            $term->is_obsolete($v);
        }
        elsif ($k eq IS_TRANSITIVE ||
               $k eq IS_SYMMETRIC  ||
               $k eq IS_ANTI_SYMMETRIC  ||
               $k eq IS_REFLEXIVE  ||
               $k eq INVERSE_OF ||
               $k eq TRANSITIVE_OVER ||
               $k eq DOMAIN ||
               $k eq RANGE) {
            my $m = lc($k);
            $term->$m($v);
        }
        elsif ($term->can("add_$k")) {
            # CONVENIENCE METHOD - map directly to object method
            warn("add method for $k");
            my $m = "add_$k";
            $term->$m($v);
        }
        elsif ($term->can($k)) {
            warn("add method for $k");
            # CONVENIENCE METHOD - map directly to object method
            $term->$k($v);
        }
        elsif ($k eq INTERSECTION_OF) {
            my $rel = stag_get($sn, TYPE);
            my $obj = stag_get($sn, TO);
            my $isect = [$rel,$obj];
            my $ns = stag_find($sn, 'namespace');
            if (!$rel) {
                shift @$isect;
            }
            my $ldef = $term->logical_definition;
            if (!$ldef) {
                $ldef = $self->apph->create_logical_definition_obj();
                $term->logical_definition($ldef);
            }
            $ldef->namespace($ns) if ($ns);
            $ldef->add_intersection($isect);
        }
        elsif ($k eq UNION_OF) {
            $term->add_equivalent_to_union_of_term($v);
        }
        elsif ($k eq DISJOINT_FROM) {
            $term->add_disjoint_from_term($v);
        }
        else {
            warn("add method for $k");
            $term->stag->add($k, $v);

#            $self->throw("don't know what to do with $k");
#            print "no $k\n";
        }
    }
    if ($self->root_to_be_added &&
	!$term->is_obsolete &&
        $stanza eq 'term') {
	my $parents = $self->g->get_parent_relationships($term->acc);
	if (!@$parents) {
	    my $root = $self->root_term || $self->throw("no root term");
            $self->g->add_relationship($root, $term->acc, IS_A);
	}
    }

#    $term->type($self->{ontology_type}) unless $term->type;
    if (!$term->name) {
#        warn("no name; using acc ".$term->acc);
#        $term->name($term->acc);
    }

    $self->g->add_term($term);
    printf STDERR "Added term %s %s\n", $term->acc, $term->name 
      if $TRACE;
#    $term;
    return ();
}

sub dbxref {
    my $self = shift;
    my $x = shift;
    $self->apph->create_xref_obj(stag_pairs($x))
}


sub e_proddb {
    my $self = shift;
    $self->proddb(shift->data);
    return;
}

sub e_prod {
    my $self = shift;
    my $tree = shift;
    my $g = $self->g;
    my $prod =
      $self->apph->create_gene_product_obj({symbol=>stag_sget($tree, PRODSYMBOL),
                                            type=>stag_sget($tree, PRODTYPE),
                                            full_name=>stag_sget($tree, PRODNAME),
                                            speciesdb=>$self->proddb,
                                      });
    my @syns = stag_get($tree, PRODSYN);
    $prod->xref->xref_key(stag_sget($tree, PRODACC));
    $prod->synonym_list(\@syns);
    my @assocs = stag_get($tree, ASSOC);
    my $taxid = stag_get($tree, PRODTAXA);
    my $species;
    if ($taxid) {
        $species =       
          $self->apph->create_species_obj({ncbi_taxa_id=>$taxid});
        $prod->species($species);

    }
    foreach my $assoc (@assocs) {
        my $acc = stag_get($assoc, TERMACC);
        if (!$acc) {
            $self->message("no accession given");
            next;
        }

        
        my $t = $g->get_term($acc);
        if (!$t) {
            if (!$self->strictorder) {
                $t = $self->apph->create_term_obj({acc=>$acc});
                $self->g->add_term($t);
            }
            else {
                $self->message("no such term $acc");
                next;
            }
        }
        my $aspect = stag_get($assoc, ASPECT);
        if ($aspect) {
            $t->set_namespace_by_code($aspect);
        }

        my @evs = stag_get($assoc, EVIDENCE);
        my $ao =
          $self->apph->create_association_obj({gene_product=>$prod,
                                               is_not=>stag_sget($assoc, IS_NOT),
                                              });
        my $date = stag_get($assoc,ASSOCDATE);
        $ao->assocdate($date) if $date;

        my $assigned_by = stag_get($assoc,SOURCE_DB);
        $ao->assigned_by($assigned_by) if $assigned_by;

        foreach my $ev (@evs) {
            my $eo =
              $self->apph->create_evidence_obj({
                                                code=>stag_sget($ev, EVCODE),
                                               });
            my @seq_xrefs = stag_get($ev, WITH),
            my @refs = stag_get($ev, REF);
            map { $eo->add_seq_xref($_) } @seq_xrefs;
            map { $eo->add_pub_xref($_) } @refs;
            $ao->add_evidence($eo);
        }
        $t->add_association($ao);
    }
    return;
}

1;