diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/Parsers/BaseExternalParser.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/Parsers/BaseExternalParser.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,269 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2011 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=cut
+
+package Bio::EnsEMBL::Funcgen::Parsers::BaseExternalParser;
+
+use strict;
+
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use Bio::EnsEMBL::Utils::Exception qw( throw );
+use Bio::EnsEMBL::Funcgen::FeatureSet;
+use Bio::EnsEMBL::Funcgen::FeatureType;
+use Bio::EnsEMBL::Analysis;
+#use Bio::EnsEMBL::Funcgen::Parsers::BaseImporter;
+#use vars qw(@ISA)
+#@ISA = ('Bio::EnsEMBL::Funcgen::Utils::Helper');
+
+use base qw(Bio::EnsEMBL::Funcgen::Parsers::BaseImporter); #@ISA change to parent with perl 5.10
+
+
+
+# Base functionality for external_feature parsers
+
+#Make this inherit from Helper?
+#Then change all the prints to logs
+
+sub new {
+  my $caller = shift;
+  my $class = ref($caller) || $caller;
+  my $self = $class->SUPER::new(@_);
+
+  #validate and set type, analysis and feature_set here
+  my ($type, $db, $archive, $import_fsets) = rearrange(['TYPE', 'DB', 'ARCHIVE', 'IMPORT_SETS'], @_);
+
+  #What is ExternalParser specific here?
+  #archive?
+  #type? is this even used?
+
+  
+  #throw('You must define a type of external_feature to import') if(! defined $type);
+
+  if (! ($db && ref($db) &&
+		 $db->isa('Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor'))){
+	throw('You must provide a valid Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor');
+  }
+
+  throw('You can only specify either -clobber|rollback or -archive, but not both') if($self->rollback && $archive);
+
+  $self->{display_name_cache} = {};
+  $self->{'db'} = $db;
+  #$self->{type} = $type;
+  $self->{archive} = $archive if defined $archive;
+
+
+  #This is not fully implemented yet and need to be validated against the config feature_set
+  #pass something like set1,set2 and split and validate each.
+  #Or do this in the calling script?
+
+  throw('-import_sets not fully implemented yet') if defined $import_fsets;
+  $self->{'import_sets'} = (defined $import_fsets) ? @{$import_fsets} : undef;
+  
+  $self->log("Parsing and loading $type ExternalFeatures");
+
+  return $self;
+
+}
+
+
+=head2 import_sets
+
+  Args       : None
+  Example    : foreach my $import_set_name(@{$self->import_sets}){ ... do the import ... }
+  Description: Getter for the list of import feature set names, defaults to all in parser config.
+  Returntype : Arrayref of import feature_set names
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub import_sets{
+  my $self = shift;
+
+  return $self->{'import_sets'} || [keys %{$self->{static_config}{feature_sets}}];
+}
+
+
+=head2 set_feature_sets
+
+  Args       : None
+  Example    : $self->set_feature_sets;
+  Description: Imports feature sets defined by import_sets.
+  Returntype : None
+  Exceptions : Throws if feature set already present and rollback or archive not set
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+#This is done after validate and store feature_types
+#Updating this will require making all external parsers use 'static_config'
+
+sub set_feature_sets{
+  my $self = shift;
+
+  throw('Must provide a set feature_set config hash') if ! defined $self->{static_config}{feature_sets};
+
+
+  my $fset_adaptor = $self->db->get_FeatureSetAdaptor;
+  my $analysis_adaptor = $self->db->get_AnalysisAdaptor;
+  
+  foreach my $fset_name(@{$self->import_sets}){
+
+	$self->log("Defining FeatureSet:\t$fset_name");  
+	my $fset = $fset_adaptor->fetch_by_name($fset_name);
+
+	#we don't need data sets for external_feature sets!
+	#Compare against config after we have merged with defined_anld_validate etc
+
+	if(defined $fset){
+	  $self->log("Found previous FeatureSet $fset_name");
+
+	  if($self->rollback){
+
+		$self->rollback_FeatureSet($fset);#Need to pass \@slices here?
+	  }
+	  elsif($self->{'archive'}){
+		my $archive_fset =  $fset_adaptor->fetch_by_name($fset_name."_v".$self->{'archive'});
+
+		if(defined $archive_fset){
+		  throw("You are trying to create an archive external feature_set which already exists:\t${fset_name}_v".$self->{archive});
+		}
+
+		my $sql = "UPDATE feature_set set name='$fset_name}_v".$self->{archive}."' where name='$fset_name'";
+		$self->db->dbc->do($sql);
+		undef $fset;
+	  }else{
+		throw("You are trying to create an external feature_set which already exists:\t$fset_name\nMaybe to want to rollback or archive?");
+	  }
+	}
+
+	#Assume using static config for now
+	#Will need to resolve this when it become generic
+	#Maybe we set outside of config!
+	#simply as analyses, feature_sets and feature_types?
+	my $fset_config = 	$self->{static_config}{feature_sets}{$fset_name}{feature_set};
+
+
+	if(! defined $fset){
+	  my ($name, $analysis, $ftype, $display_label, $desc);	  
+	  my $fset_analysis_key = (exists ${$fset_config}{-analysis})      ? '-analysis'      : '-ANALYSIS';
+	  my $fset_name_key     = (exists ${$fset_config}{-name})          ? '-name'          : '-NAME';
+	  my $fset_ftype_key    = (exists ${$fset_config}{-feature_type})  ? '-feature_type'  : '-FEATURE_TYPE';
+	  my $fset_dlabel_key   = (exists ${$fset_config}{-display_label}) ? '-display_label' : '-DISPLAY_LABEL';
+	  my $fset_desc_key     = (exists ${$fset_config}{-description})   ? '-description'   : '-DESCRIPTION';
+	  my $display_name      = (exists ${$fset_config}{$fset_dlabel_key}) ? $fset_config->{$fset_dlabel_key} : $fset_name;
+	  #fset config name be different from key name
+	  my $fs_name           = (exists ${$fset_config}{$fset_name_key}) ? $fset_config->{$fset_name_key} : $fset_name;
+	  #warn if they are different?
+	  
+	  
+	  #Can't just deref config hash here as we need to deref the nested feature_type and analysis attrs
+	  
+	  $fset = Bio::EnsEMBL::Funcgen::FeatureSet->new(
+													 -name         => $fs_name,
+													 -feature_class=> 'external',
+													 -analysis     => ${$fset_config->{$fset_analysis_key}},
+													 -feature_type => ${$fset_config->{$fset_ftype_key}},
+													 -display_label => $display_name,
+													 -description   => $fset_config->{$fset_desc_key}
+													);
+
+	  ($fset) = @{$self->db->get_FeatureSetAdaptor->store($fset)};
+	}
+
+	#Now replace config hash with object
+	#Will this reset in hash or just locally?
+	#$fset_config = $fset;
+	$self->{static_config}{feature_sets}{$fset_name}{feature_set} = $fset;
+  }
+
+  return;
+}
+
+#Can't use this anymore as we have to use static_config for all parsers which use set_feature_sets
+
+#
+#=head2 validate_and_store_feature_types
+#
+#  Args       : None
+#  Example    : $self->validate_and_store_feature_types;
+#  Description: Imports feature types defined by import_sets.
+#  Returntype : None
+#  Exceptions : None
+#  Caller     : General
+#  Status     : High Risk - Now using BaseImporter::validate_and_store_config for vista
+#
+#=cut
+#
+##Change all external parsers to use BaseImporter::validate_and_store_config
+#
+#sub validate_and_store_feature_types{
+#  my $self = shift;
+#
+#  #This currently only stores ftype associated with the feature_sets
+#  #Havent't we done this already in the InputSet parser
+#  #Need to write BaseImporter and inherit from there.
+#
+#  #InputSet does all loading, but depends on 'user_config'
+#  #Where as we are using hardcoded config here
+#  #Which are import_sets currently defaults to feature_sets keys
+#
+#  #we could simply call this static_config and let user_config over-write static config with warnings?
+#  #on an key by key basis? (top level only?)
+#
+#
+#  my $ftype_adaptor = $self->db->get_FeatureTypeAdaptor;
+#
+#  foreach my $import_set(@{$self->import_sets}){
+#
+#	my $ftype_config = ${$self->{static_config}{feature_sets}{$import_set}{feature_type}};
+#	my $ftype = $ftype_adaptor->fetch_by_name($ftype_config->{'name'});
+#
+#	$self->log("Validating $import_set FeatureType:\t".$ftype_config->{'name'});
+#
+#	if(! defined $ftype){
+#	  $self->log("FeatureType '".$ftype_config->{'name'}."' for external feature_set ".$self->{'type'}." not present");
+#	  $self->log("Storing using type hash definitions");
+#	
+#	  $ftype = Bio::EnsEMBL::Funcgen::FeatureType->new(
+#													   -name => $ftype_config->{'name'},
+#													   -class => $ftype_config->{'class'},
+#													   -description => $ftype_config->{'description'},
+#													  );
+#	  ($ftype) = @{$ftype_adaptor->store($ftype)};
+#	}
+#
+#	#Replace hash config with object
+#	$self->{static_config}{feature_types}{$ftype_config->{'name'}} = $ftype;
+#  }
+#
+#  return;
+#}
+#
+
+
+
+
+
+
+
+1;