Add classification groups to the config check page.

lib/BIGSdb/ConfigCheckPage.pm

@@ -38,6 +38,7 @@ sub print_content {
 	if ( $self->{'system'}->{'dbtype'} eq 'isolates' ) {
 		$self->_check_locus_databases;
 		$self->_check_scheme_databases;
+		$self->_check_classification_scheme_databases;
 	} else {
 		$self->_check_client_databases;
 	}
@@ -222,6 +223,61 @@ sub _check_scheme_databases {
 	return;
 }
 
+sub _check_classification_scheme_databases {
+	my ($self) = @_;
+	say q(<div class="box resultstable">);
+	say q(<h2>Classification scheme databases</h2>);
+	my $cschemes =
+	  $self->{'datastore'}
+	  ->run_query( 'SELECT id FROM classification_schemes ORDER BY id', undef, { fetch => 'col_arrayref' } );
+	my $td = 1;
+	if (@$cschemes) {
+		say q(<div class="scrollable"><table class="resultstable"><tr><th>Classification scheme</th>)
+		  . q(<th>Scheme</th><th>Database</th><th>Host</th><th>Port</th><th>Table</th><th>Database accessible</th>)
+		  . q(<th>Seqdef classification scheme id</th><th>Classification data</th></tr>);
+		foreach my $cscheme_id (@$cschemes) {
+			my $cscheme_info = $self->{'datastore'}->get_classification_scheme_info($cscheme_id);
+			my $scheme_info  = $self->{'datastore'}->get_scheme_info( $cscheme_info->{'scheme_id'} );
+			$cscheme_info->{'name'}       =~ s/&/&amp;/gx;
+			$scheme_info->{'description'} =~ s/&/&amp;/gx;
+			print qq(<tr class="td$td"><td>$cscheme_info->{'id'}: $cscheme_info->{'name'}</td><td>)
+			  . ("$scheme_info->{'id'}: $scheme_info->{'description'}")
+			  . q(</td><td>)
+			  . ( $scheme_info->{'dbase_name'} // q() )
+			  . q(</td><td>)
+			  . ( $scheme_info->{'dbase_host'} // $self->{'system'}->{'host'} )
+			  . q(</td><td>)
+			  . ( $scheme_info->{'dbase_port'} // $self->{'system'}->{'port'} )
+			  . q(</td><td>)
+			  . ( $scheme_info->{'dbase_table'} // q() )
+			  . q(</td><td>);
+			if ( $self->{'datastore'}->get_classification_scheme($cscheme_id)->get_db ) {
+				print q(<span class="statusgood fa fa-check"></span>);
+			} else {
+				print q(<span class="statusbad fa fa-times"></span>);
+			}
+			print qq(</td><td>$cscheme_info->{'seqdef_cscheme_id'}</td><td>);
+			my $seqdef_db = $self->{'datastore'}->get_scheme( $cscheme_info->{'scheme_id'} )->get_db;
+			my $exists    = $self->{'datastore'}->run_query(
+				'SELECT EXISTS(SELECT * FROM classification_group_profiles WHERE cg_scheme_id=?)',
+				$cscheme_info->{'seqdef_cscheme_id'},
+				{ db => $seqdef_db }
+			);
+			if ($exists) {
+				print q(<span class="statusgood fa fa-check"></span>);
+			} else {
+				print q(<span class="statusbad fa fa-times"></span>);
+			}
+			my $classification_data = say q(</td></tr>);
+			$td = $td == 1 ? 2 : 1;
+		}
+		say q(</table></div></div>);
+	} else {
+		say q(<p>No schemes with databases defined.</p>);
+	}
+	return;
+}
+
 sub _check_client_databases {
 	my ($self) = @_;
 	my $client_dbs =

lib/BIGSdb/IsolateInfoPage.pm

@@ -504,21 +504,25 @@ sub _get_classification_group_data {
 				foreach my $group_id (@$groups) {
 					my $isolate_count = $self->{'datastore'}->run_query(
 						"SELECT COUNT(*) FROM $view WHERE $view.id IN (SELECT id FROM $scheme_table WHERE $pk IN "
-						  . "(SELECT profile_id FROM $cscheme_table WHERE group_id=?)) AND new_version IS NULL",
+						  . "(SELECT profile_id FROM $cscheme_table WHERE group_id=?)) AND new_version IS NULL"
+						,
 						$group_id
 					);
 					if ( $isolate_count > 1 ) {
 						my $url = "$self->{'system'}->{'script_name'}?db=$self->{'instance'}&page=query&"
 						  . "designation_field1=cg_$cscheme->{'id'}_group&designation_value1=$group_id&submit=1";
-						$cg_buffer .=
-						  qq(<dt>group</dt><dd><a href="$url">$group_id</a> ($isolate_count isolates)</dd>\n);
+						$cg_buffer .= qq(group: <a href="$url">$group_id ($isolate_count isolates)</a><br />\n);
 					}
 				}
 			}
 		}
 		if ($cg_buffer) {
-			$cg_buffer = qq(<div style="float:left"><h3>Scheme: $cscheme->{'name'}</h3>\n)
-			  . qq(<dl class="data">$cg_buffer</dl></div>\n);
+			my $plural = $cscheme->{'inclusion_threshold'} == 1 ? q() : q(es);
+			$cg_buffer =
+			    qq(<div style="float:left;margin-right:2em"><h3>Scheme: $cscheme->{'name'}</h3>\n)
+			  . qq(<p>$scheme_info->{'description'}<br />$cscheme->{'inclusion_threshold'} mismatch$plural.)
+			  . q(<br />Single-linkage cluster.<br />)
+			  . qq($cg_buffer</div>\n);
 			$buffer .= $cg_buffer;
 		}
 	}