genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 26)

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

Modified Files:
	AM_Spots.pm 
Log Message:
new

Index: AM_Spots.pm
===================================================================
RCS file: /cvsroot/genex/genex-server/Genex/AM_Spots/AM_Spots.pm,v
retrieving revision 1.30
retrieving revision 1.31
diff -C2 -d -r1.30 -r1.31
*** AM_Spots.pm	15 Nov 2002 21:55:07 -0000	1.30
--- AM_Spots.pm	23 Nov 2002 10:18:12 -0000	1.31
***************
*** 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;
***************
*** 938,942 ****
  =item insert_matrix($class,%args)

! This method inserts the data for the object into the database
  specified by the DB handle $dbh. To use this method, create a blank
  container object with C<new()> (for class C<Bio::Genex::AM_Spots> the
--- 938,942 ----
  =item insert_matrix($class,%args)

! This method inserts a matrix of data  into the database
  specified by the DB handle $dbh. To use this method, create a blank
  container object with C<new()> (for class C<Bio::Genex::AM_Spots> the
***************
*** 953,956 ****
--- 953,957 ----
    $physicalbioassay->insert_db($dbh);

+ 
  Supported %args

***************
*** 961,976 ****
  an active database handle

- =item * fkey
- 
- the container objects primary key that will be entered in the foreign
- key slot for each matrix row
- 
  =item * matrix

  an array ref holding the matrix

! =item * name

- the person responisible for the insertion

  =back
--- 962,974 ----
  an active database handle

  =item * matrix

  an array ref holding the matrix

! =item * fkey
! 
! the container objects primary key that will be entered in the foreign
! key slot for each matrix row

  =back
***************
*** 983,986 ****
--- 981,985 ----
  container object.

+ 
  =cut

***************
*** 994,1002 ****
    my ($pack,$file,$line,$sub) = caller(0);
    push(@error_args, caller=>"$pack:$file:$line:$sub");

    my $lt_pkey = $args{fkey};
-   my $matrix = $args{matrix};
    # first we ensure that the container instance is really in the DB
!   my $sql = $dbh->create_select_sql( COLUMNS=>['pba_pk'],
                                FROM=>[Bio::Genex::PhysicalBioAssay->table_or_viewname($dbh)],
                                WHERE=>qq[pba_pk='$lt_pkey'],
--- 993,1008 ----
    my ($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;

    my $lt_pkey = $args{fkey};
    # first we ensure that the container instance is really in the DB
!   $sql = $dbh->create_select_sql( COLUMNS=>['pba_pk'],
                                FROM=>[Bio::Genex::PhysicalBioAssay->table_or_viewname($dbh)],
                                WHERE=>qq[pba_pk='$lt_pkey'],
***************
*** 1008,1015 ****
      if not defined $ref or not scalar @{$ref};

    # ok to proceed with insert
!   my $header = shift @{$matrix};
    push(@{$header},'pba_fk','ams_pk');

    # pre-fetch the next value of the sequence
    my $seq = 'GENEX_ID_SEQ';
--- 1014,1023 ----
      if not defined $ref or not scalar @{$ref};

+ 
    # ok to proceed with insert
!   # add lookup table fkey and primary key to each row
    push(@{$header},'pba_fk','ams_pk');

+ 
    # pre-fetch the next value of the sequence
    my $seq = 'GENEX_ID_SEQ';
***************
*** 1028,1032 ****
--- 1036,1043 ----
              message=>"Couldn't prepare insert sql",
              sql=>$sql);
+ 
+   my $count;
    foreach my $row (@{$matrix}) {
+     $count++;
      $seq_sth->execute()
        or $dbh->error(@error_args,
***************
*** 1043,1052 ****
      # DBI won't re-run the SQL until we finish
      $seq_sth->finish();
      $sth->execute(@{$row},$lt_pkey,$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();
--- 1054,1069 ----
      # DBI won't re-run the SQL until we finish
      $seq_sth->finish();
+ 
      $sth->execute(@{$row},$lt_pkey,$pkey->[0])
        or $dbh->error(@error_args,
              message=>"Couldn't execute insert sql with args: "
!             . join(',',@{$row},$lt_pkey,$pkey->[0]),
              sth=>$sth,
              sql=>$sql);
+ 
+ 
+     print STDERR "Handled $count Bio::Genex::AM_Spots objects
+ "
+       if $DEBUG and $COUNT and ($count % $COUNT == 0);
    }
    my $ga_db = Bio::Genex::GenexAdmin->new();

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genex-cvs-commit Mailing List for GeneX Gene Expression Database (Page 26)

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