analysis: fix tiering dependencies, #TASK-7610

Author: pfurio

opencga-analysis/src/main/java/org/opencb/opencga/analysis/clinical/tiering/TieringInterpretationAnalysisExecutor.java

@@ -26,7 +26,7 @@
 import org.opencb.biodata.models.clinical.pedigree.Pedigree;
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.models.variant.Variant;
-import org.opencb.biodata.tools.clinical.TieringClinicalVariantCreator;
+import org.opencb.biodata.tools.clinical.tiering.TieringClinicalVariantCreator;
 import org.opencb.biodata.tools.pedigree.ModeOfInheritance;
 import org.opencb.commons.datastore.core.Query;
 import org.opencb.commons.datastore.core.QueryOptions;

opencga-analysis/src/test/java/org/opencb/opencga/analysis/tools/ToolFactoryTest.java

@@ -18,15 +18,11 @@
 
 import org.junit.Test;
 import org.junit.experimental.categories.Category;
-import org.opencb.commons.datastore.core.ObjectMap;
-import org.opencb.opencga.analysis.customTool.CustomToolExecutor;
 import org.opencb.opencga.core.exceptions.ToolException;
 import org.opencb.opencga.core.models.common.Enums;
 import org.opencb.opencga.core.testclassification.duration.ShortTests;
-import org.opencb.opencga.core.tools.ToolParams;
 import org.opencb.opencga.core.tools.annotations.Tool;
 
-import java.lang.reflect.Field;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
@@ -59,37 +55,6 @@ protected void run() throws Exception {
         }
     }
 
-    @Test
-    public void test() throws ToolException {
-//        ObjectMap params = new ObjectMap("params", new ObjectMap("commandLine", "blablabla"));
-        ObjectMap params2 = new ObjectMap("params", new ObjectMap("params", new ObjectMap("key", "value")).append("commandLine", "blablabla"));
-
-        CustomToolExecutor customToolExecutor = new CustomToolExecutor();
-
-        ToolParams toolParams = null;
-        for (Field field : CustomToolExecutor.class.getDeclaredFields()) {
-            if (field.isAnnotationPresent(org.opencb.opencga.core.tools.annotations.ToolParams.class)
-                    && ToolParams.class.isAssignableFrom(field.getType())) {
-                try {
-                    field.setAccessible(true);
-                    toolParams = (ToolParams) field.get(customToolExecutor);
-                    if (toolParams == null) {
-                        toolParams = (ToolParams) field.getType().newInstance();
-                        field.set(customToolExecutor, toolParams);
-                    }
-                    break;
-                } catch (IllegalAccessException | InstantiationException e) {
-                    throw new ToolException("Unexpected error reading ToolParams");
-                }
-            }
-        }
-        System.out.println("toolParams.toJson() = " + toolParams.toJson());
-//        toolParams.updateParams(params);
-        System.out.println("toolParams.toJson() = " + toolParams.toJson());
-        toolParams.updateParams(params2);
-        System.out.println("toolParams.toJson() = " + toolParams.toJson());
-    }
-
     @Test
     public void testFactoryById() throws ToolException {
         ToolFactory toolFactory = new ToolFactory();