Parameters Tester updated. Untested webservice code. generate xsd/wsdl?

[jabaws.git] / testsrc / compbio / runner / structure / RNAalifoldParametersTester.java

diff --git a/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java b/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java
index 9c15537..21ed5d4 100644 (file)
--- a/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java
+++ b/testsrc/compbio/runner/structure/RNAalifoldParametersTester.java
@@ -68,6 +68,9 @@ public class RNAalifoldParametersTester {
                                        new RunnerConfigMarshaller<RNAalifold>(RunnerConfig.class);
                        rnaalifoldConfig = rnaalifoldmarsh.read(new FileInputStream(new File(
                                        rnaalifoldConfigFile)), RunnerConfig.class);
+                       // set Name value separator
+                       rnaalifoldConfig.setPrmSeparator(" ");
+                       log.info("prmSeparator: " + rnaalifoldConfig.getPrmSeparator());
                        rnaalifoldOpc = new OptionCombinator(rnaalifoldConfig);
                        
                        log.info("Num options: " + rnaalifoldOpc.getAllOptions().size());
@@ -125,6 +128,31 @@ public class RNAalifoldParametersTester {
        public void testOptions() {
                test(rnaalifoldOpc.getAllOptions());
        }
+       
+       @Test(groups = { AllTestSuit.test_group_runner })
+       public void testOptionPairs() throws ResultNotAvailableException {
+               List<Option<?>> pair = new ArrayList<Option<?>>();
+               List<Option<?>> options = rnaalifoldOpc.getAllOptions();
+               int numpairs = 0;
+               for (int i = 0; i<options.size(); i++) {
+                       for (int j = i; j<options.size(); j++) {
+                               if (i != j) {
+                                       //System.out.println("special numOptions: " + options.size());
+                                       //System.out.println("special loop varaibles:-  (i,j): (" + i + "," + j +")");
+                                       pair.clear();
+                                       pair.add(options.get(i)); pair.add(options.get(j));
+                                       log.info("option pair to test: " + pair);
+                                       // I want to catch ResultNotAvailableException here so 
+                                       // I can return a list of imcompatable options but
+                                       // singleTest calls a fail() method...
+                                       // can i fail the test and continue running?
+                                       test(pair);
+                                       
+                                       //System.out.println("special numpairstested: " + ++numpairs);
+                               }
+                       }
+               }
+       }
 
        @Test(groups = { AllTestSuit.test_group_runner })
        public void testParameters() {
@@ -141,6 +169,7 @@ public class RNAalifoldParametersTester {
                test(options);
        }
        
+       /*
        void test(Map<Parameter<?>, String> paramValue) {
                List<Parameter<?>> paramList = new ArrayList<Parameter<?>>(paramValue
                                .keySet());
@@ -152,6 +181,7 @@ public class RNAalifoldParametersTester {
                }
                log.info("NUMBER OF COMBINATION TESTED: " + paramValue.size());
        }
+       */
        
        void test(List<? extends Option<?>> params) {
                for (int i = 0; i < params.size(); i++) {
@@ -162,6 +192,20 @@ public class RNAalifoldParametersTester {
                log.info("NUMBER OF COMBINATION TESTED: " + params.size());
        }
        
+       @Test
+       void singleParamTest() {
+               //List<Parameter<?>> params = rnaalifoldOpc.getAllParameters();
+               //System.out.println("special: params: " + params);
+               
+               //List<String> args = rnaalifoldOpc.argumentsToCommandString(params);
+               List<String> args = new ArrayList<String>();
+               args.add("-T 37"); args.add("-S 1.07"); args.add("--stochBT_en=10");
+               args.add("--MEA=1");
+               System.out.println("special: args: " + args);
+               singleTest(args);
+               
+       }
+       
        void singleTest(List<String> params) {
                try {
                        log.info("Using arguments: " + params);