4 levels of hierarchy

modules/Bio/EnsEMBL/Hive/ProcessWithParams.pm

@@ -31,6 +31,11 @@ package Bio::EnsEMBL::Hive::ProcessWithParams;
 use strict;
 use base ('Bio::EnsEMBL::Hive::Process');
 
+sub strict_hash_format {    # This public virtual must be redefined to "return 0;" in all inheriting classes
+                            # that want more flexibility for the format of parameters() or input_id()
+    return 1;
+}
+
 sub param_init {    # normally will run automatically on the first execution of $self->param(),
                     # but you can enforce it by running manually, optionally supplying the default values
                     
@@ -38,23 +43,15 @@ sub param_init {    # normally will run automatically on the first execution of
 
     if( !$self->{'_param_hash'} or scalar(@_) ) {
 
-        my $defaults = scalar(@_) ? { @_ } : {};    # built-in defaults have the lowest precedence
+        my $defaults_hash    = scalar(@_) ? { @_ } : {};            # module-wide built-in defaults have the lowest precedence (will always be the same for this module)
 
-        my $parameters = eval($self->parameters()) || {};
-        if($@) {
-            die "The module '".ref($self)."' for analysis '".$self->analysis->logic_name()
-                ."' assumes analysis.parameters should evaluate into a {'param'=>'value'} hashref."
-                ." The current value is '".$self->parameters()."'\n";
-        }
+        my $meta_params_hash = $self->_parse_meta();                # then come the pipeline-wide parameters from the 'meta' table (define things common to all modules in this pipeline)
 
-        my $input_id   = eval($self->input_id()) || {};
-        if($@) {
-            die "The module '".ref($self)."' for analysis '".$self->analysis->logic_name()
-                ."' assumes analysis_job.input_id should evaluate into a {'param'=>'value'} hashref."
-                ." The current value is '".$self->input_id()."'\n";
-        }
+        my $parameters_hash  = $self->_parse_string('parameters');  # analysis-wide 'parameters' are even more specific (can be defined differently for several occurence of the same module)
 
-        $self->{'_param_hash'} = { %$defaults, %$parameters, %$input_id };
+        my $input_id_hash    = $self->_parse_string('input_id');    # job-specific 'input_id' parameters have the highest precedence
+
+        $self->{'_param_hash'} = { %$defaults_hash, %$meta_params_hash, %$parameters_hash, %$input_id_hash };
     }
 }
 
@@ -71,4 +68,44 @@ sub param {
     return $self->{'_param_hash'}{$param_name};
 }
 
+#--------------------------------------------[private methods]----------------------------------------------
+
+sub _parse_string {
+    my ($self, $method) = @_;
+
+    my $string = $self->$method();
+
+    if($self->strict_hash_format() or $string=~/^\{.*\}$/) {
+        my $param_hash = eval($string) || {};
+        if($@ or (ref($param_hash) ne 'HASH')) {
+            die "The module '".ref($self)."' for analysis '".$self->analysis->logic_name()
+                ."' assumes analysis.$method should evaluate into a {'param'=>'value'} hashref."
+                ." The current value is '$string'\n";
+        }
+        return $param_hash;
+    } else {
+        return {};
+    }
+}
+
+    # Unfortunately, MetaContainer is useless for us, as we need to load all the parameters in one go
+    #
+sub _parse_meta {
+    my $self = shift @_;
+
+    my %meta_params_hash = ();
+
+        # Here we are assuming that meta_keys are unique.
+        # If they are not, you'll be getting the value with the highest meta_id.
+        #
+    my $sth = $self->db->dbc()->prepare("SELECT meta_key, meta_value FROM meta ORDER BY meta_id");
+    $sth->execute();
+    while (my ($meta_key, $meta_value)=$sth->fetchrow_array()) {
+        $meta_params_hash{$meta_key} = $meta_value;
+    }
+    $sth->finish();
+
+    return \%meta_params_hash;
+}
+
 1;