[Genex-cvs-commit] genex-server/Genex/Reporter Reporter.pm,1.6,1.7

[<jas...@us...>]

Update of /cvsroot/genex/genex-server/Genex/Reporter
In directory sc8-pr-cvs1:/tmp/cvs-serv9614/Reporter

Modified Files:
	Reporter.pm 
Log Message:
added insert_matrix()


Index: Reporter.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/Reporter/Reporter.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Reporter.pm	15 Nov 2002 21:55:17 -0000	1.6
--- Reporter.pm	21 Nov 2002 12:28:48 -0000	1.7
***************
*** 1166,1169 ****
--- 1166,1282 ----
  
  
+ =item insert_matrix($class,%args)
+ 
+ 
+ This method inserts a matrix of data into the database specified by
+ the DB handle $dbh. Class C<Bio::Genex::Reporter> has no foreign keys of
+ type 'lookup table', so C<insert_matrix> may be invoked as a ordinary
+ class method.
+ 
+   my $matrix = some_method_returning_data();
+   Bio::Genex::Reporter->insert_matrix(dbh=>$dbh,matrix=>$matrix);
+ 
+ 
+ 
+ Supported %args
+ 
+ =over
+ 
+ =item * dbh
+ 
+ an active database handle
+ 
+ =item * matrix
+ 
+ an array ref holding the matrix
+ 
+ 
+ 
+ =back
+ 
+ B<NOTE:> You must log into the DB with a user/password that has INSERT
+ priveleges in the DB, otherwise you will get a DBI error.
+ 
+ 
+ 
+ =cut
+ 
+ sub insert_matrix {
+   my ($class,%args) = @_;
+   my $dbh = $args{dbh};
+   assert_dbh($dbh);
+ 
+   my $table_name = Bio::Genex::Reporter->table_or_viewname($dbh);
+   my @error_args = ();
+   my ($pack,$file,$line,$sub) = caller(0);
+   push(@error_args, caller=>"$pack:$file:$line:$sub");
+   my $matrix = $args{matrix};
+   $dbh->error(@error_args,
+                message=>"Must supply array reference for 'matrix'",
+                no_errstr=>1,
+               )
+     unless ref($matrix) eq 'ARRAY';
+   my $header = shift @{$matrix};
+   my $sql;
+ 
+ 
+ 
+   # add primary key to each row
+   push(@{$header},'rep_pk');
+ 
+ 
+   # pre-fetch the next value of the sequence
+   my $seq = 'GENEX_ID_SEQ';
+   my $seq_sql = qq[SELECT nextval('"$seq"'::text)];
+   my $seq_sth = $dbh->prepare($seq_sql)
+     or $dbh->error(@error_args,
+                    sql=>$seq_sql,
+                    message=>"Couldn't prepare nextval for sequence $seq",
+                   );
+ 
+   $sql = $dbh->create_insert_sql($table_name,
+                            $header,
+                           );
+   my $sth = $dbh->prepare($sql)
+     or $dbh->error(@error_args,
+             message=>"Couldn't prepare insert sql",
+             sql=>$sql);
+   foreach my $row (@{$matrix}) {
+     $seq_sth->execute()
+       or $dbh->error(@error_args,
+             message=>"Couldn't execute nextval from sequence $seq",
+             sth=>$seq_sth,
+             sql=>$seq_sql);
+     my $pkey = $seq_sth->fetchrow_arrayref();
+     $dbh->error(@error_args,
+             message=>"Couldn't fetch nextval from sequence $seq",
+             sth=>$seq_sth,
+             sql=>$seq_sql)
+       unless defined $pkey && $pkey->[0];
+ 
+     # DBI won't re-run the SQL until we finish
+     $seq_sth->finish();
+ 
+     $sth->execute(@{$row},$pkey->[0])
+       or $dbh->error(@error_args,
+             message=>"Couldn't execute insert sql with args: "
+             . join(',',@{$row},$pkey->[0]),
+             sth=>$sth,
+             sql=>$sql);
+ 
+ 
+   }
+   my $ga_db = Bio::Genex::GenexAdmin->new();
+   my $description = "inserted " . scalar @{$matrix} . " Bio::Genex::Reporter objects";
+   $ga_db->description($description);
+   $ga_db->insert_db($dbh);
+ 
+   $dbh->error(@error_args,
+ 	    message=>"Couldn't insert GenexAdmin record")
+     if $dbh->err;
+ 
+   return 1;
+ }
+ 
  # ObjectTemplate automagically creates a new() method for us 
  # that method invokes $self->initialize() after first setting all