Add Bio::DB::Expression modules

Imported from bioperl-live 746e2c23ecc7b05341a42d976fe276271a3fe682
bioperl · Sep 17, 2018 · e6f767e · e6f767e
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diff --git a/Bio/DB/Expression.pm b/Bio/DB/Expression.pm
@@ -0,0 +1,213 @@
+#
+# BioPerl module for Bio::DB::Expression
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org> 
+#
+# Cared for by Allen Day <allenday@ucla.edu>
+#
+# Copyright Allen Day
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::DB::Expression - DESCRIPTION of Object
+
+=head1 SYNOPSIS
+
+  use Bio::DB::Expression;
+  my $db = Bio::DB::Expression->new( -source => 'geo' );
+  my @platforms = $db->get_platforms();
+  foreach my $platform ( @platforms ) {
+    my @datasets = $platform->get_datasets();
+    foreach my $dataset ( @datasets ) {
+      my @samples = $dataset->get_samples();
+      foreach my $sample ( @samples ) {
+        #...
+      }
+    }
+  }
+
+=head1 DESCRIPTION
+
+Describe the object here
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  bioperl-l@bioperl.org                  - General discussion
+  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
+
+=head2 Support 
+
+Please direct usage questions or support issues to the mailing list:
+
+I<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and 
+reponsive experts will be able look at the problem and quickly 
+address it. Please include a thorough description of the problem 
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+  https://github.com/bioperl/bioperl-live/issues
+
+=head1 AUTHOR - Allen Day
+
+Email allenday@ucla.edu
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::DB::Expression;
+use strict;
+use base qw(Bio::Root::HTTPget Bio::Root::Root);
+use Bio::Root::HTTPget;
+our $DefaultSource = 'geo';
+
+=head2 new()
+
+ Usage   : my $obj = Bio::DB::Expression->new();
+ Function: Builds a new Bio::DB::Expression object 
+ Returns : an instance of Bio::DB::Expression
+ Args    :
+
+
+=cut
+
+sub new {
+  my($class,@args) = @_;
+
+  if( $class =~ /Bio::DB::Expression::(\S+)/ ) {
+    my ($self) = $class->SUPER::new(@args);
+    $self->_initialize(@args);
+    return $self;
+  } else {
+    my %param = @args;
+    @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
+    my $source = $param{'-source'} || $DefaultSource;
+
+    $source = "\L$source";	# normalize capitalization to lower case
+
+    # normalize capitalization
+    return unless( $class->_load_expression_module($source) );
+    return "Bio::DB::Expression::$source"->new(@args);
+  }
+}
+
+=head2 get_platforms()
+
+ Usage   :
+ Function:
+ Example :
+ Returns : a list of Bio::Expression::Platform objects
+ Args    :
+
+=cut
+
+sub get_platforms {
+  my ($self,@args) = @_;
+  $self->throw_not_implemented();
+}
+
+=head2 get_samples()
+
+ Usage   :
+ Function:
+ Example :
+ Returns : a list of Bio::Expression::Sample objects
+ Args    :
+
+=cut
+
+sub get_samples {
+  my ($self,@args) = @_;
+  $self->throw_not_implemented();
+}
+
+=head2 get_contacts()
+
+ Usage   :
+ Function:
+ Example :
+ Returns : a list of Bio::Expression::Contact objects
+ Args    :
+
+=cut
+
+sub get_contacts {
+  my ($self,@args) = @_;
+  $self->throw_not_implemented();
+}
+
+=head2 get_datasets()
+
+ Usage   :
+ Function:
+ Example :
+ Returns : a list of Bio::Expression::DataSet objects
+ Args    :
+
+=cut
+
+sub get_datasets {
+  my ($self,@args) = @_;
+  $self->throw_not_implemented();
+}
+
+
+
+
+=head2 _load_expression_module
+
+ Title   : _load_expression_module
+ Usage   : *INTERNAL Bio::DB::Expression stuff*
+ Function: Loads up (like use) a module at run time on demand
+ Example :
+ Returns :
+ Args    :
+
+=cut
+
+sub _load_expression_module {
+    my ($self, $source) = @_;
+    my $module = "Bio::DB::Expression::" . $source;
+    my $ok;
+
+    eval { $ok = $self->_load_module($module) };
+    if ( $@ ) {
+	print STDERR $@;
+	print STDERR <<END;
+$self: $source cannot be found
+Exception $@
+For more information about the Bio::DB::Expression system please see
+the Bio::DB::Expression docs.  This includes ways of checking for 
+formats at compile time, not run time.
+END
+  ;
+    }
+    return $ok;
+}
+
+
+1;