Query reading is now more consistent, previously we would end up with a mixed bag of some "real" and some "query" bonds. We now get out all query bonds which broke the test. The correct test is that there are 6 query bonds of type SINGLE/DOUBLE, the other query bonds match order=1.

johnmay · johnmay · commit dd4ab311bf71 · 2020-07-10T13:52:11.000+01:00
diff --git a/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java b/storage/ctab/src/test/java/org/openscience/cdk/io/MDLV2000ReaderTest.java
@@ -1,4 +1,4 @@
-/* 
+/*
  * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
  *                    2014  Mark B Vine (orcid:0000-0002-7794-0426)
  *
@@ -977,8 +977,9 @@ public void testQueryBondType8() throws Exception {
             if (atom.getSymbol().equals("Ir")) {
                 for (IBond bond : atc.getConnectedBondsList(atom)) {
                     if (bond instanceof QueryBond) {
+                      if (((QueryBond) bond).getExpression().type() == Expr.Type.TRUE) {
                         queryBondCount++;
-                        assertSame(((QueryBond) bond).getExpression().type(), Expr.Type.TRUE);
+                      }
                     }
                 }
             }
@@ -1000,8 +1001,9 @@ public void testQueryBondType6() throws Exception {
 
         for (IBond bond : atc.bonds()) {
             if (bond instanceof QueryBond) {
-                queryBondCount++;
-                assertSame(((QueryBond) bond).getExpression().type(), Expr.Type.SINGLE_OR_AROMATIC);
+                if (((QueryBond) bond).getExpression().type() == Expr.Type.SINGLE_OR_AROMATIC) {
+                    queryBondCount++;
+                }
             }
         }
         Assert.assertEquals("Expecting six 'query' bond types", 6, queryBondCount);
@@ -1762,7 +1764,7 @@ public void testMassDiff() throws Exception {
             Assert.assertEquals(2, atom.getMassNumber().intValue());
         }
     }
-	
+
     @Test
     public void testBadAtomCoordinateFormat() throws Exception {
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-/*`
	`1`	`+/*`
`2`	`2`	`* Copyright (C) 2003-2007 The Chemistry Development Kit (CDK) project`
`3`	`3`	`* 2014 Mark B Vine (orcid:0000-0002-7794-0426)`
`4`	`4`	`*`
`@@ -977,8 +977,9 @@ public void testQueryBondType8() throws Exception {`
`977`	`977`	`if (atom.getSymbol().equals("Ir")) {`
`978`	`978`	`for (IBond bond : atc.getConnectedBondsList(atom)) {`
`979`	`979`	`if (bond instanceof QueryBond) {`
	`980`	`+ if (((QueryBond) bond).getExpression().type() == Expr.Type.TRUE) {`
`980`	`981`	`queryBondCount++;`
`981`		`- assertSame(((QueryBond) bond).getExpression().type(), Expr.Type.TRUE);`
	`982`	`+ }`
`982`	`983`	`}`
`983`	`984`	`}`
`984`	`985`	`}`
`@@ -1000,8 +1001,9 @@ public void testQueryBondType6() throws Exception {`
`1000`	`1001`
`1001`	`1002`	`for (IBond bond : atc.bonds()) {`
`1002`	`1003`	`if (bond instanceof QueryBond) {`
`1003`		`- queryBondCount++;`
`1004`		`- assertSame(((QueryBond) bond).getExpression().type(), Expr.Type.SINGLE_OR_AROMATIC);`
	`1004`	`+ if (((QueryBond) bond).getExpression().type() == Expr.Type.SINGLE_OR_AROMATIC) {`
	`1005`	`+ queryBondCount++;`
	`1006`	`+ }`
`1005`	`1007`	`}`
`1006`	`1008`	`}`
`1007`	`1009`	`Assert.assertEquals("Expecting six 'query' bond types", 6, queryBondCount);`
`@@ -1762,7 +1764,7 @@ public void testMassDiff() throws Exception {`
`1762`	`1764`	`Assert.assertEquals(2, atom.getMassNumber().intValue());`
`1763`	`1765`	`}`
`1764`	`1766`	`}`
`1765`		`-`
	`1767`	`+`
`1766`	`1768`	`@Test`
`1767`	`1769`	`public void testBadAtomCoordinateFormat() throws Exception {`
`1768`	`1770`