Fixed QC: don't try to check ID patterns, if no pattern is defined (e…

….g. when the IDs have a DataSource defined in the Derby file)
marvinm2 · May 18, 2017 · 0def8f7 · 0def8f7
1 parent 05d5fff
commit 0def8f7
Showing 1 changed file with 12 additions and 9 deletions.
diff --git a/org.bridgedb.tools.qc/src/org/bridgedb/tools/qc/PatternChecker.java b/org.bridgedb.tools.qc/src/org/bridgedb/tools/qc/PatternChecker.java
@@ -72,16 +72,19 @@ public void run (File f) throws SQLException, IDMapperException
 		while (rs.next())
 		{
 			String id = rs.getString(1);
-			DataSource ds = DataSource.getExistingBySystemCode(rs.getString(2));
-			if (patterns.get(ds) == null) continue; // skip if there is no pattern defined.
-
-			Set<DataSource> matches = DataSourcePatterns.getDataSourceMatches(id);
-			if (!matches.contains(ds))
-			{
-				if (missExamples.get(ds).size() < 10) missExamples.put(ds, id);
-				misses.add (ds);
+			String syscode = rs.getString(2);
+			if (DataSource.systemCodeExists(syscode)) {
+				DataSource ds = DataSource.getExistingBySystemCode(syscode);
+				if (patterns.get(ds) == null) continue; // skip if there is no pattern defined.
+
+				Set<DataSource> matches = DataSourcePatterns.getDataSourceMatches(id);
+				if (!matches.contains(ds))
+				{
+					if (missExamples.get(ds).size() < 10) missExamples.put(ds, id);
+					misses.add (ds);
+				}
+				totals.add (ds);
 			}
-			totals.add (ds);
 		}