genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 25)

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Update of /cvsroot/genex/genex-server/Genex/ExternalDatabase
In directory sc8-pr-cvs1:/tmp/cvs-serv5789/Genex/ExternalDatabase

Modified Files:
	ExternalDatabase.pm 
Log Message:
new

Index: ExternalDatabase.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/ExternalDatabase/ExternalDatabase.pm,v
retrieving revision 1.31
retrieving revision 1.32
diff -C2 -d -r1.31 -r1.32
*** ExternalDatabase.pm	15 Nov 2002 21:55:12 -0000	1.31
--- ExternalDatabase.pm	23 Nov 2002 10:18:15 -0000	1.32
***************
*** 22,26 ****

! use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $FKEYS $COLUMN2NAME $NAME2COLUMN $COLUMN_NAMES %_CACHE $USE_CACHE $LIMIT $FKEY_OBJ2RAW $TABLE2PKEY $UNIQUE_COLUMNS $SUPER_CLASSES $TABLE_TYPE $PKEY_NAME $TABLE_NAME $DEBUG $TABLE_NAME_VIEW);

  require Exporter;
--- 22,26 ----

! use vars qw($VERSION @ISA @EXPORT @EXPORT_OK $FKEYS $COLUMN2NAME $NAME2COLUMN $COLUMN_NAMES %_CACHE $USE_CACHE $LIMIT $FKEY_OBJ2RAW $TABLE2PKEY $UNIQUE_COLUMNS $SUPER_CLASSES $TABLE_TYPE $PKEY_NAME $TABLE_NAME $DEBUG $TABLE_NAME_VIEW $COUNT);

  require Exporter;
***************
*** 960,963 ****
--- 960,1082 ----
  }

+ 
+ =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::ExternalDatabase> has no foreign keys of
+ type 'lookup table', so C<insert_matrix> may be invoked as a ordinary
+ class method.
+ 
+   my $matrix = some_method_returning_data();
+   Bio::Genex::ExternalDatabase->insert_matrix(dbh=>$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 $table_name = Bio::Genex::ExternalDatabase->table_or_viewname($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},'ed_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);
+ 
+   my $count;
+   foreach my $row (@{$matrix}) {
+     $count++;
+     $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);
+ 
+ 
+     print STDERR "Handled $count Bio::Genex::ExternalDatabase objects
+ "
+       if $DEBUG and $COUNT and ($count % $COUNT == 0);
+   }
+   my $ga_db = Bio::Genex::GenexAdmin->new();
+   my $description = "inserted " . scalar @{$matrix} . " Bio::Genex::ExternalDatabase 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 

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genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 25)

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