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lib/CXGN/BreedersToolbox/Projects.pm

@@ -5,30 +5,31 @@ use Moose;
 use Data::Dumper;
 use Try::Tiny;
 use SGN::Model::Cvterm;
+use CXGN::People::Schema;
 use CXGN::People::Roles;
 use JSON;
 use Encode;
 use CXGN::BrAPI::v2::ExternalReferences;
 use Try::Tiny;
 
 has 'schema' => (
-		 is       => 'rw',
-		 isa      => 'DBIx::Class::Schema',
-		);
+    is       => 'rw',
+    isa      => 'DBIx::Class::Schema',
+    );
 
 has 'id' => (
-	isa => 'Maybe[Int]',
-	is => 'rw',
+    isa => 'Maybe[Int]',
+    is => 'rw',
 );
 
 has 'name' => (
     isa => 'Str',
-	is => 'rw',
+    is => 'rw',
 );
 
 has 'description' => (
     isa => 'Maybe[Str]',
-	is => 'rw',
+    is => 'rw',
 );
 
 has 'external_references' => (
@@ -541,7 +542,10 @@ sub store_breeding_program {
     # Add new program if no id supplied
     if (!$id) {
         try {
-            my $role = CXGN::People::Roles->new({bcs_schema=>$self->schema});
+	    my $dbh = $self->schema()->storage()->dbh();
+	    my $people_schema = CXGN::People::Schema->connect( sub { $dbh->clone() } );
+
+            my $role = CXGN::People::Roles->new({ people_schema => $people_schema});
             my $error = $role->add_sp_role($name);
             if ($error){
                 die $error;
@@ -599,7 +603,9 @@ sub store_breeding_program {
             my $old_program = $schema->resultset("Project::Project")->search({ project_id => $id });
             my $old_name = $old_program->first->name();
 
-            my $role = CXGN::People::Roles->new({bcs_schema=>$self->schema});
+	    my $dbh = $self->schema()->storage()->dbh();
+	    my $people_schema = CXGN::People::Schema->connect( sub { $dbh->clone } );
+            my $role = CXGN::People::Roles->new({ people_schema => $people_schema });
             my $error = $role->update_sp_role($name,$old_name);
             if ($error){
                 die $error;

lib/CXGN/People/Roles.pm

@@ -5,7 +5,7 @@ CXGN::People::Roles - helper class for people's roles
 
 =head1 SYNOPSYS
 
- my $person_roles = CXGN::Person::Roles->new( { bcs_schema => $schema } );
+ my $person_roles = CXGN::Person::Roles->new( { people_schema => $schema } );
 
  etc.
 
@@ -26,15 +26,20 @@ use Data::Dumper;
 use Text::Unidecode;
 use List::MoreUtils qw /any /;
 
-has 'bcs_schema' => (
-	isa => 'Bio::Chado::Schema',
-	is => 'rw',
-);
+has 'bcs_schema' => (  # deprecated
+    isa => 'Bio::Chado::Schema',
+    is => 'rw',
+    );
+
+has 'people_schema' => (
+    isa => 'CXGN::People::Schema',
+    is => 'rw',
+    );
 
 sub add_sp_role {
 	my $self = shift;
 	my $name = shift;
-	my $dbh = $self->bcs_schema->storage->dbh;
+	my $dbh = $self->people_schema->storage->dbh;
 
 	my $q="SELECT sp_role_id FROM sgn_people.sp_roles where name=?;";
 	my $sth = $dbh->prepare($q);
@@ -55,33 +60,75 @@ sub add_sp_role {
 }
 
 sub update_sp_role {
-	my $self = shift;
-	my $new_name = shift;
+    my $self = shift;
+    my $new_name = shift;
     my $old_name = shift;
-	my $dbh = $self->bcs_schema->storage->dbh;
-
-	my $q="SELECT sp_role_id FROM sgn_people.sp_roles where name=?;";
+    my $dbh = $self->people_schema->storage->dbh;
+
+    my $q="SELECT sp_role_id FROM sgn_people.sp_roles where name=?;";
+    my $sth = $dbh->prepare($q);
+    $sth->execute($old_name);
+    my $count = $sth->rows;
+    if ($count < 1){
+	print STDERR "No role with that name exists.\n";
+	return;
+    }
+    eval {
+	my $q="UPDATE sgn_people.sp_roles SET name = ? WHERE name = ?;";
 	my $sth = $dbh->prepare($q);
-	$sth->execute($old_name);
-	my $count = $sth->rows;
-	if ($count < 1){
-		print STDERR "No role with that name exists.\n";
-		return;
-	}
-	eval {
-		my $q="UPDATE sgn_people.sp_roles SET name = ? WHERE name = ?;";
-		my $sth = $dbh->prepare($q);
-		$sth->execute($new_name,$old_name);
-	};
-	if ($@) {
-		return "An error occurred while updating an existing role. ($@)";
-	}
+	$sth->execute($new_name,$old_name);
+    };
+    if ($@) {
+	return "An error occurred while updating an existing role. ($@)";
+    }
+}
+
+sub role_hash {
+    my $self = shift;
+    my %roles;
+    my $rs1 = $self->people_schema()->resultset("SpRole")->search( { } );
+    while (my $row = $rs1->next()) {
+	$roles{$row->sp_role_id} = $row->name();
+    }
+    return %roles;
+}
+
+sub list_roles {
+    my $self = shift;
+    my $sp_person_id = shift;
+
+    my $rs2;
+
+    if ($sp_person_id) { 
+	$rs2 = $self->people_schema->resultset("SpPerson")->search(
+	    { censor => 0, disabled => undef, 'me.sp_person_id' => $sp_person_id },
+	    { join => 'sp_person_roles',
+	      '+select' => ['sp_person_roles.sp_role_id', 'sp_person_roles.sp_person_role_id' ],
+	      '+as'     => ['sp_role_id', 'sp_person_role_id' ],
+	      order_by => 'sp_role_id' });
+    }
+    else {
+	$rs2 = $self->people_schema->resultset("SpPerson")->search(
+	    { censor => 0, disabled => undef },
+	    { join => 'sp_person_roles',
+	      '+select' => ['sp_person_roles.sp_role_id', 'sp_person_roles.sp_person_role_id' ],
+	      '+as'     => ['sp_role_id', 'sp_person_role_id' ],
+	      order_by => 'sp_role_id' });
+    }	
+
+    my @rows;
+
+    while (my $row= $rs2->next()) {
+	push @rows, $row;
+    }
+
+    return @rows;
 }
 
 sub get_breeding_program_roles {
 	my $self = shift;
 	my $ascii_chars = shift;
-	my $dbh = $self->bcs_schema->storage->dbh;
+	my $dbh = $self->people_schema->storage->dbh;
 	my @breeding_program_roles;
 	my $q="SELECT username, sp_person_id, name, censor FROM sgn_people.sp_person
 	JOIN sgn_people.sp_person_roles using(sp_person_id)
@@ -104,7 +151,7 @@ sub add_sp_person_role {
 	my $self = shift;
 	my $sp_person_id = shift;
 	my $sp_role_id = shift;
-	my $dbh = $self->bcs_schema->storage->dbh;
+	my $dbh = $self->people_schema->storage->dbh;
 	my $q = "INSERT INTO sgn_people.sp_person_roles (sp_person_id, sp_role_id) VALUES (?,?);";
 	my $sth = $dbh->prepare($q);
 	$sth->execute($sp_person_id, $sp_role_id);
@@ -113,7 +160,7 @@ sub add_sp_person_role {
 
 sub get_sp_persons {
 	my $self = shift;
-	my $dbh = $self->bcs_schema->storage->dbh;
+	my $dbh = $self->people_schema->storage->dbh;
 	my @sp_persons;
 	my $q="SELECT username, sp_person_id FROM sgn_people.sp_person WHERE disabled IS NULL and censor = 0 ORDER BY username ASC;";
 	my $sth = $dbh->prepare($q);
@@ -126,7 +173,7 @@ sub get_sp_persons {
 
 sub get_sp_roles {
 	my $self = shift;
-	my $dbh = $self->bcs_schema->storage->dbh;
+	my $dbh = $self->people_schema->storage->dbh;
 	my @sp_roles;
 	my $q="SELECT name, sp_role_id FROM sgn_people.sp_roles;";
 	my $sth = $dbh->prepare($q);