Merge branch 'JWS-29' into develop

[jabaws.git] / testsrc / compbio / metadata / AllTestSuit.java

diff --git a/testsrc/compbio/metadata/AllTestSuit.java b/testsrc/compbio/metadata/AllTestSuit.java
index 2c045cc..92f1748 100644 (file)
--- a/testsrc/compbio/metadata/AllTestSuit.java
+++ b/testsrc/compbio/metadata/AllTestSuit.java
@@ -32,35 +32,36 @@ public class AllTestSuit {
                        .getPresets(ClustalW.class);\r
        public static final RunnerConfig<ClustalW> CLUSTAL_PARAMETERS = Util\r
                        .getSupportedOptions(ClustalW.class);\r
-       public static final LimitsManager<ClustalW> CLUSTAL_LIMITS = Util\r
-                       .getLimits(ClustalW.class);\r
+       public static final LimitsManager<ClustalW> CLUSTAL_LIMITS = compbio.engine.client.Util\r
+                       .getLimits(new ClustalW().getType());\r
 \r
        public static final PresetManager<Tcoffee> TCOFFEE_PRESETS = Util\r
                        .getPresets(Tcoffee.class);\r
        public static final RunnerConfig<Tcoffee> TCOFFEE_PARAMETERS = Util\r
                        .getSupportedOptions(Tcoffee.class);\r
-       public static final LimitsManager<Tcoffee> TCOFFEE_LIMITS = Util\r
-                       .getLimits(Tcoffee.class);\r
+       public static final LimitsManager<Tcoffee> TCOFFEE_LIMITS = compbio.engine.client.Util\r
+                       .getLimits(new Tcoffee().getType());\r
 \r
        public static final PresetManager<Muscle> MUSCLE_PRESETS = Util\r
                        .getPresets(Muscle.class);\r
        public static final RunnerConfig<Muscle> MUSCLE_PARAMETERS = Util\r
                        .getSupportedOptions(Muscle.class);\r
-       public static final LimitsManager<Muscle> MUSCLE_LIMITS = Util\r
-                       .getLimits(Muscle.class);\r
+       public static final LimitsManager<Muscle> MUSCLE_LIMITS = compbio.engine.client.Util\r
+                       .getLimits(new Muscle().getType());\r
 \r
        public final static String test_group_cluster = "cluster";\r
        public final static String test_group_runner = "runner";\r
        public final static String test_group_non_windows = "non_windows";\r
+       public final static String test_group_windows_only = "windows_only";\r
        public final static String test_group_engine = "engine";\r
        public final static String test_group_long = "performance";\r
+       public final static String test_group_webservices = "webservices";\r
 \r
        /*\r
         * For this to work execution must start from the project directory!\r
         */\r
        public static final String CURRENT_DIRECTORY = SysPrefs\r
-                       .getCurrentDirectory()\r
-                       + File.separator;\r
+                       .getCurrentDirectory() + File.separator;\r
 \r
        public static final String TEST_DATA_PATH = "testsrc" + File.separator\r
                        + "testdata" + File.separator;\r
@@ -71,13 +72,16 @@ public class AllTestSuit {
        // For cluster execution paths MUST BE ABSOLUTE as cluster hosts will not be\r
        // able to access the task otherwise\r
        public static final String OUTPUT_DIR_ABSOLUTE = AllTestSuit.CURRENT_DIRECTORY\r
-                       + File.separator + "jobsout" + File.separator;\r
+                       + File.separator + "local_jobsout" + File.separator;\r
 \r
        public static final String RUNNER_TEST_LOGGER = "RunnerLogger";\r
 \r
        public static final String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
                        + "TO1381.fasta";\r
 \r
+       public static final String test_alignment_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
+                       + "TO1381.fasta.aln";\r
+\r
        public static final String test_input_real = AllTestSuit.TEST_DATA_PATH_ABSOLUTE\r
                        + "50x500Protein.fasta";\r
 \r