Inchi does not officially support fractions of seconds timeout in options. For safety, input which is formatted accordingly will be reformatted to pass next higher integer value.

Glur, Marco · Glur, Marco · commit d4091b3db59e · 2020-07-30T10:50:05.000+02:00
diff --git a/storage/inchi/src/main/java/org/openscience/cdk/inchi/JniInChIInputAdapter.java b/storage/inchi/src/main/java/org/openscience/cdk/inchi/JniInChIInputAdapter.java
@@ -27,7 +27,6 @@
 import net.sf.jniinchi.JniInchiException;
 import net.sf.jniinchi.JniInchiInput;
 
-import java.text.DecimalFormat;
 import java.util.List;
 import java.util.StringTokenizer;
 
@@ -55,23 +54,11 @@ public JniInChIInputAdapter(List<INCHI_OPTION> options) throws JniInchiException
 
     private static boolean isTimeoutOptions(String op) {
         if (op == null || op.length() < 2) return false;
-        int pos = 0;
-        int len = op.length();
-        if (op.charAt(pos) == 'W')
-            pos++;
-        while (pos < len && Character.isDigit(op.charAt(pos)))
-            pos++;
-        if (pos < len && (op.charAt(pos) == '.' || op.charAt(pos) == ','))
-            pos++;
-        while (pos < len && Character.isDigit(op.charAt(pos)))
-            pos++;
-        return pos == len;
-    }
+        return op.charAt(0) == 'W';
 
-    private static boolean isSubSecondTimeout(String op) {
-        return op.indexOf('.') >= 0 || op.indexOf(',') >= 0;
     }
 
+
     private static String checkOptions(final String ops) throws JniInchiException {
         if (ops == null) {
             throw new IllegalArgumentException("Null options");
@@ -96,18 +83,14 @@ private static String checkOptions(final String ops) throws JniInchiException {
                     sbOptions.append(" ");
                 }
             } else if (isTimeoutOptions(op)) {
-                // only reformat if we actually have a decimal
-                if (isSubSecondTimeout(op)) {
-                    // because the JNI-InChI library is expecting an platform number, format it as such
-	                Double time = Double.parseDouble(op.substring(1));
-	                DecimalFormat format = new DecimalFormat("#.##");
-	                sbOptions.append(FLAG_CHAR).append('W').append(format.format(time));
-                } else {
-                    sbOptions.append(FLAG_CHAR).append(op);
-                }
-                hasUserSpecifiedTimeout = true;
-                if (tok.hasMoreTokens()) {
-                    sbOptions.append(" ");
+                final double time = Math.ceil(Double.parseDouble(op.substring(1)));
+                // fix #653: safer to use whole seconds, rounded to next bigger integer
+                if (time >= 0.0) {
+                    sbOptions.append(FLAG_CHAR).append(String.format("W%.0f", time));
+                    hasUserSpecifiedTimeout = true;
+                    if (tok.hasMoreTokens()) {
+                        sbOptions.append(" ");
+                    }
                 }
             }
             // 1,5 tautomer option
diff --git a/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java b/storage/inchi/src/test/java/org/openscience/cdk/inchi/InChIGeneratorTest.java
@@ -896,11 +896,7 @@ public void s_penta_2_3_diene_expl_h() throws Exception {
         }
     }
 
-    // if this test hits the timeout it's likely the users Locale is mixed, the
-    // InChI library was loaded in one mode and java is in another, the issue
-    // is InChI takes timeout in seconds and fractional seconds will be either
-    // 0.1 or 0,1 depending on locale.
-    @Test(timeout = 500)
+    @Test(timeout = 1500)
     public void timeout() throws Exception {
         IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();
         SmilesParser smipar = new SmilesParser(bldr);

Original file line number	Diff line number	Diff line change
`@@ -896,11 +896,7 @@ public void s_penta_2_3_diene_expl_h() throws Exception {`
`896`	`896`	`}`
`897`	`897`	`}`
`898`	`898`
`899`		`- // if this test hits the timeout it's likely the users Locale is mixed, the`
`900`		`- // InChI library was loaded in one mode and java is in another, the issue`
`901`		`- // is InChI takes timeout in seconds and fractional seconds will be either`
`902`		`- // 0.1 or 0,1 depending on locale.`
`903`		`- @Test(timeout = 500)`
	`899`	`+ @Test(timeout = 1500)`
`904`	`900`	`public void timeout() throws Exception {`
`905`	`901`	`IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();`
`906`	`902`	`SmilesParser smipar = new SmilesParser(bldr);`