File: chado-build-schema.pl

package info (click to toggle)
libchado-perl 1.31-6
  • links: PTS, VCS
  • area: main
  • in suites: bookworm, bullseye, sid
  • size: 44,716 kB
  • sloc: sql: 282,721; xml: 192,553; perl: 25,524; sh: 102; python: 73; makefile: 57
file content (343 lines) | stat: -rwxr-xr-x 9,483 bytes parent folder | download | duplicates (4)
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
#!/usr/bin/env perl 

use strict;
use warnings;
use Data::Stag;
use FileHandle;
use Getopt::Long;
use Tk;
use SQL::Translator;
use Data::Dumper;

my ($HELP, $OUTFILE, $INFILE, $ONLY_SQL);

my $rows_of_stuff=28;

GetOptions(
  'help'      => \$HELP,
  'outfile=s' => \$OUTFILE,
  'infile=s'  => \$INFILE,
  'only_sql'  => \$ONLY_SQL,
);

if ($HELP) {
    system ("pod2text", $0);
    exit(0);
}

my $SCHEMA_FILE  = $OUTFILE || "chado_schema.sql";
my $metafile     = $INFILE  || "chado-module-metadata.xml";

my $schema_md = Data::Stag->parse($metafile);

my $module_dir = $schema_md->get('modules/source/@/path');
my @modules = $schema_md->get('modules/module');
my @components = $schema_md->get('modules/module/component');
my %module_h = map {$_->sget('@/id') => $_} (@modules, @components);
my @module_ids = map {$_->sget('@/id')} @modules;

# Tk - root frame
my $mw = MainWindow->new;
$mw->title("Chado Admin Tool");
my $mframe = $mw->Frame;

my $row = 0;
my $column1 = 1;
my %button_h = ();
foreach my $id (@module_ids) {
    my $mod = $module_h{$id};
    attach_module_checkbutton($id);

    # components associated with this module
    my @components = $mod->get('component');
    foreach my $component (@components) {
        my $c_id = $component->sget('@/id');
        attach_module_checkbutton($c_id, 1);
    }

}

my $translate_to;

$mframe->Checkbutton(-text=>"SQL only",
                     -variable => \$ONLY_SQL)->grid;
$mframe->Button(-text=>"Select All",
                -command=>\&select_all)->grid(-column=>1,-row=>$rows_of_stuff+2);
$mframe->Button(-text=>"Deselect All",
                -command=>\&deselect_all)->grid(-column=>2,-row=>$rows_of_stuff+2);

$mframe->Button(-text=>"Create Pg Schema",
                -command=>\&create_schema)->grid(-column=>3,-row=>$rows_of_stuff+2);

my @optionlist = ('Oracle','MySQL','Diagram','GraphViz','HTML');
$mframe->Label( -text=>"Translate to:")->grid(-column=>4,-row=>$rows_of_stuff+2);
$mframe->Optionmenu (-options => \@optionlist,
                -variable => \$translate_to)->grid(-column=>5,-row=>$rows_of_stuff+2);
$mframe->Button(-text=>"Translate Schema",
                -command=>\&translate_schema)->grid(-column=>6,-row=>$rows_of_stuff+2);



$mframe->pack(-side=>'bottom');
MainLoop;

exit 0;
#

sub attach_module_checkbutton {
    my $id = shift;
    my $indent = shift || 0;
    $row++;

    my $col;
    if ($row == $rows_of_stuff+1) {
        $col+=4;
        $row=1;
        $column1=0;
    } elsif ($column1) {
        $col=0;
    } else {
        $col=4;
    }


    my $mod = $module_h{$id};
    my $desc = $mod->sget('description');
    my $status = $mod->sget('status');
    my $is_required = $mod->sget('@/required') ? 1 : 0;

    # button frame: contains button and help ? button
    my $bframe = $mframe->Frame;
    {
        $bframe->Label(-text=>".." x $indent)->pack(-anchor=>'w',-side=>'left')
          if $indent;
        
        my $text = $id;
        my $cb = $bframe->Checkbutton(-text=>$text,
                                      -command=>sub {
                                          module_checkbox_action($id);
                                      });
        $cb->{'Value'} = $is_required;
        $cb->pack(-anchor=>'w',-side=>'left',-fill=>'x',-padx=>0);
        $button_h{$id} = $cb;
    }

    $bframe->grid(-column=>$col++,-row=>$row,-sticky=>'w');

    $mframe->Label(-text=>substr($desc,0,40))->grid(-column=>$col++,-row=>$row,-sticky=>'w');

    my $help_but =
      $mframe->Button(-text=>'?',
                      -foreground=>'red',
                      -command=>sub {
                          my $help_dialog = $mframe->messageBox(-message=>$mod->xml);
                          return;
                      });
    $help_but->grid(-column=>$col++,-row=>$row);

    if ($status) {
        $mframe->Label(-text=>$status->sget('@/code'),
                       -foreground=>'blue')->grid(-column=>$col,-row=>$row);
    }
    $col++;
}

sub module_checkbox_action {
    my $id = shift;
    my $mod = $module_h{$id};
    my $button = $button_h{$id};
    if ($button->{'Value'}) {
        # -- SELECT --
        my @dependencies = $mod->get('dependency/@/to');
        foreach my $dep_id (@dependencies) {
            my $b2 = $button_h{$dep_id};
            if (!$b2->{'Value'}) {
                $b2->select;
                # recursively set dependencies
                module_checkbox_action($dep_id);
            }
        }
    }
    else {
        # -- DESELECT --
        my @dependents = 
          map {
              $_->sget('@/id')
          } $schema_md->qmatch('module',
                               ('dependency/@/to'=>$id));
        foreach my $dep_id (@dependents) {
            my $b2 = $button_h{$dep_id};
            if ($b2->{'Value'}) {
                $b2->deselect;
                # recursively deselect dependents
                module_checkbox_action($dep_id);
            }
        }

        # deselect subcomponents
        my @components = $mod->get('component/@/id');
        foreach my $c_id (@components) {
            my $b2 = $button_h{$c_id};
            if ($b2->{'Value'}) {
                $b2->deselect;
                # recursively set dependencies
                module_checkbox_action($c_id);
            }
        }
    }
    return;
}

sub create_schema {
    my @sql_lines = ();
    foreach my $id (@module_ids) {
        my $mod = $module_h{$id};
        if ($button_h{$id}->{'Value'}) {
            push(@sql_lines, read_source($mod));
        }

        # components associated with this module
        my @components = $mod->get('component');
        foreach my $component (@components) {
            my $c_id = $component->sget('@/id');
            if ($button_h{$c_id}->{'Value'}) {
                push(@sql_lines, read_source($component));
                if (my @subs = $component->get('component')) {
                    foreach my $subcomp (@subs) {
                        push(@sql_lines, read_source($subcomp));
                    }
                }

            }

        }
    }
    my $fh = FileHandle->new(">$SCHEMA_FILE");
    if ($fh) {
        print $fh join('',@sql_lines);
        $fh->close;
        #print `cat $SCHEMA_FILE`;
        $mw->messageBox(-message=>"Pg schema created in file $SCHEMA_FILE");
    } else {
        $mw->messageBox(-message=>"cannot write to $SCHEMA_FILE");
    }
}

sub translate_schema {
    $ONLY_SQL = 1;
    create_schema();

    $mw->messageBox(-message=>"Please wait for the translation (it can take several minutes)");

    my $TRANS_FILE = $SCHEMA_FILE."_$translate_to";
    my $translator = SQL::Translator->new(
        show_warnings       => 1,
    );
   
    my $output = $translator->translate(
        from                => 'PostgreSQL',
        to                  => $translate_to,
        filename            => $SCHEMA_FILE,
    ) or warn $translator->error; 

    my $fh = FileHandle->new(">$TRANS_FILE");
    if ($fh) {
        print $fh $output;
        $fh->close;
        $mw->messageBox(-message=>"$translate_to schema created in file $TRANS_FILE");
    } else {
        $mw->messageBox(-message=>"cannot write to $TRANS_FILE");
    }
}

sub read_source {
    my $mod = shift;
    my $id = $mod->sget('@/id');
    my @sources = $mod->get_source;
    my @lines = ();
    foreach my $source (@sources) {
        my $type = $source->sget('@/type');
        my $path = $source->sget('@/path');
        if ($ONLY_SQL && ($type ne 'sql' || $path =~ /view/ || $path =~ /bridge/ ) ) {
            print STDERR "Skipping source $type $path for $id\n";
            next;
        }
        elsif ($type ne 'sql' && $type ne 'plpgsql') {
            print STDERR "Skipping source $type $path for $id\n";
            next;
        }
        my $f = "$module_dir/$path";
        my $fh=FileHandle->new($f);        
        if ($fh) {
            push(@lines, <$fh>);
            $fh->close;
        }
        else {
            $mw->messageBox(-message=>"cannot find $f");
        }
    }
    return @lines;
}

sub select_all {
    foreach (keys %button_h) {
       $button_h{$_}->{'Value'} = 1;
    }
    return;
}

sub deselect_all {
    foreach (keys %button_h) {
       $button_h{$_}->{'Value'} = 0;
    }
    return;
}


sub usage {
    system( 'pod2usage', $0 );
    exit(0);
}


=pod

=head1 NAME

chado-build-schema.pl - PerlTk application to build and translate a chado schema

=head1 SYNOPSIS

  % chado-build-schema.pl [options]

=head1 COMMAND-LINE OPTIONS

    --help              This usage statement
    --infile            The name of the metadata xml file
                          (default: chado-module-metadata.xml)
    --outfile           The name of the output ddl file
                          (default: chado_schema.sql)
    --only_sql          Only use pure sql (ie, no views or functions)


=head1 DESCRIPTION

This is a perlTk application to help uses interactively build
a chado data definition langauge (ddl/sql) file.  By default, it
builds a PostgreSQL compatible file, but by making use of SQL::Translator,
it can translate the ddl to Oracle or MySQL ddl, or create schema diagrams
or html documentation.  Use of this application is not required if 
the standard default chado schema will be used.

=head1 AUTHORS

Chris Mungall, Scott Cain E<lt>cain@cshl.eduE<gt>

Copyright (c) 2005

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.


=cut