test code to make sure the tutorials on the core api page run okay

da44116e · Ian Longden · 5ce05bf5 · da44116e
Commit da44116e authored Nov 17, 2011 by Ian Longden
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misc-scripts/core_tutorial_test/test_code_from_html.pl misc-scripts/core_tutorial_test/test_code_from_html.pl +143 -0

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--- a/misc-scripts/core_tutorial_test/test_code_from_html.pl
+++ b/misc-scripts/core_tutorial_test/test_code_from_html.pl
+use strict;
+use Getopt::Long;
+
+my $path;
+my $host;
+my $user;
+
+my $ret = Getopt::Long::GetOptions ('path=s' => \$path,
+                                    'host=s' => \$host,
+                                    'user=s' => \$user,
+                                    'help'   => sub { usage(); exit(0); } );
+
+if(!defined $path){
+  print "you must defined the path to the ensembl webcode\n";
+  usage();
+  exit(0);
+}
+
+my $file = $path."/ensembl-webcode/htdocs/info/docs/api/core/core_tutorial.html";
+
+my $code_count = 0;
+$user ||= "ensro";
+$host ||= "ens-staging";
+my $header =(<<"HED");
+####### start of insertion #########
+use Bio::EnsEMBL::Registry;
+my \$registry = 'Bio::EnsEMBL::Registry';
+
+\$registry->load_registry_from_db(
+    -host => "$host",
+    -user => "$user");
+HED
+
+my $slice_adaptor = (<<'SLI');
+my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' );
+SLI
+
+open(HTML,"<$file") || die "Could not open $file\n";
+
+my $code_mode = 0;
+my $code = "";
+while (my $line = <HTML>){
+  chomp $line;
+#  print $line."DUDE\n";
+  if($code_mode){
+    if($line =~ m/\<\/pre\>/){
+      $code_mode = 0;
+      process_code();
+      $code = "";
+    }
+    else{
+      $code .= "\n".$line;
+    }
+  }
+  elsif($line =~ m/pre.*code/){
+#    print "CODEMODE*******\n"; 
+    $code_mode = 1;
+  }
+
+}
+
+close HTML;
+
+sub process_code{
+
+  $code_count++;
+  $file = "test".$code_count.".pl";
+  open(PERL,">".$file) or die "Could not open $file for writing\n";
+
+  $code =~ s/\&gt\;/\>/g;
+  my $prefix = "";
+  if(!($code =~ /load_registry_from_db/m)){
+    $prefix = $header;
+    if(!($code =~ /my\s*\$slice_adaptor/)){
+      $prefix .= $slice_adaptor;
+      if(!($code =~ /fetch_by_region/)){
+	$prefix .= 'my $slice = $slice_adaptor->fetch_by_region( "clone", "AL031658.11" );'."\n";
+      }
+    }
+    if(!($code =~ /my\s*\$cs_adaptor/)){
+      $prefix .= 'my $cs_adaptor = $registry->get_adaptor( "Human", "Core", "CoordSystem" );'."\n";;
+    }
+    if(!($code =~ /my\s*\$gene_adaptor/)){
+      $prefix .= 'my $gene_adaptor = $registry->get_adaptor( "Human", "Core", "Gene" );'."\n";;
+    }
+    if($code =~ /\$feature\-\>/ and !( $code =~ /\$feature_adaptor/) ){
+      $prefix .= 'my $feat_adaptor = $registry->get_adaptor( "Human", "Core", "Gene" );'."\n";
+      $prefix .= 'my $feature = $feat_adaptor->fetch_by_display_label("COG6");'."\n";
+    }
+    if($code =~ /\$transcript\-\>/ and ! ( $code =~ /\$transcript_adaptor/) ){
+      $prefix .= 'my $transcript_adaptor = $registry->get_adaptor( "Human", "Core", "transcript" );'."\n";
+      $prefix .= 'my $transcript = $transcript_adaptor->fetch_by_stable_id("ENST00000380152");'."\n";
+    }
+    if($code =~ /\$translation\-\>/ and ! ( $code =~ /\$translation_adaptor/) ){
+      $prefix .= 'my $transcript_adaptor = $registry->get_adaptor( "Human", "Core", "transcript" );'."\n";
+      $prefix .= 'my $transcript = $transcript_adaptor->fetch_by_stable_id("ENST00000380152");'."\n";
+      $prefix .= 'my $translation = $transcript->translation;'."\n";
+    }
+    if( $code =~ /\$marker\-\>/ and ! ( $code =~ /\$marker_adaptor/) ){
+      $prefix .= 'my $marker_adaptor = $registry->get_adaptor( "Human", "Core", "marker" );'."\n";
+      $prefix .= 'my $marker = $marker_adaptor->fetch_all_by_synonym("D9S1038E")->[0];'."\n";
+    }
+  }
+  $code = $prefix."####### end of insertion#########\n".$code;
+  print PERL $code."\n";;
+  close PERL;
+  sleep 2;
+#  print "CODE".$code."\n";
+
+  my $test_val = system("perl $file >& /dev/null");
+#  print "VAL is $test_val\n";
+
+
+ # my $test_val =  eval {$code};
+
+  if($test_val){
+    print "file $file FAILED  $test_val\n";
+  }
+  else{
+    print "file $file OKAY    $test_val\n";
+  }
+}
+
+sub usage {
+  print << "EOF";
+  perl test_code_from_html.pl
+
+  This script will strip and create seperate perl files for any block in the html
+  that is in surrounded by <pre class="code"> ... </pre>
+  The script adds registry code etc at the start if is not a full code example.
+  These perl scripts are then executed and the status of this run reports if the
+  code as successfully executed.
+
+  -path    The path to the ensembl-webcode directory (Must be set)
+
+  -user    User name to be used for the mysql instance
+
+  -host    Host name of the mysql instance (defualt ens-staging)
+
+  i.e. perl test_code_from_html -path ~/src
+
+EOF
+}