Merge branch 'development'

# Conflicts: # pom.xml
bd2kccd · Oct 29, 2019 · 23c030a · 23c030a
2 parents f51519a + 4ab1a70
commit 23c030a
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Showing 3 changed files with 40 additions and 4 deletions.
diff --git a/pom.xml b/pom.xml
@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-cmd</artifactId>
-    <version>1.1.1</version>
+    <version>1.1.2</version>
     <packaging>jar</packaging>
 
     <properties>
@@ -144,7 +144,7 @@
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-log4j12</artifactId>
-            <version>1.7.26</version>
+            <version>1.7.28</version>
         </dependency>
         <dependency>
             <groupId>junit</groupId>
@@ -153,4 +153,4 @@
         </dependency>
     </dependencies>
 
-</project>
+</project>
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
@@ -18,7 +18,10 @@
  */
 package edu.pitt.dbmi.causal.cmd;
 
+import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
 import edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory;
+import edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper;
+import edu.cmu.tetrad.algcomparison.utils.UsesScoreWrapper;
 import edu.cmu.tetrad.data.DataType;
 import edu.cmu.tetrad.util.ParamDescription;
 import edu.cmu.tetrad.util.ParamDescriptions;
@@ -30,6 +33,7 @@
 import java.io.Serializable;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedList;
 import java.util.List;
@@ -273,7 +277,7 @@ private static ParseOptions getValidOptions(String[] args, Options options) thro
 
         List<String> params = new LinkedList<>();
         try {
-            params.addAll(AlgorithmFactory.create(algorithmClass, indTestClass, scoreClass).getParameters());
+            params.addAll(getAllParameters(AlgorithmFactory.create(algorithmClass, indTestClass, scoreClass)));
         } catch (IllegalAccessException | InstantiationException exception) {
             throw new CmdParserException(parseOptions, exception);
         }
@@ -301,6 +305,36 @@ private static ParseOptions getValidOptions(String[] args, Options options) thro
         return parseOptions;
     }
 
+    /**
+     * Get the parameters for the algorithm, the algorithm's test and the
+     * algorithm's score.
+     *
+     * @param algorithm to get parameters from
+     * @return list of parameters for the algorithm, test and score
+     */
+    private static List<String> getAllParameters(Algorithm algorithm) {
+        if (algorithm == null) {
+            return Collections.EMPTY_LIST;
+        }
+
+        List<String> params = new LinkedList<>();
+
+        // add algorithm parameters
+        params.addAll(algorithm.getParameters());
+
+        // add the algorithm test parameters, if any
+        if (algorithm instanceof TakesIndependenceWrapper) {
+            params.addAll(((TakesIndependenceWrapper) algorithm).getIndependenceWrapper().getParameters());
+        }
+
+        // add the algorithm's score parameters, if any
+        if (algorithm instanceof UsesScoreWrapper) {
+            params.addAll(((UsesScoreWrapper) algorithm).getScoreWrapper().getParameters());
+        }
+
+        return params;
+    }
+
     private static void addGraphManipulationOptions(Options opts) {
         opts.addOption(CmdOptions.getInstance().getLongOption(CmdParams.CHOOSE_DAG_IN_PATTERN));
         opts.addOption(CmdOptions.getInstance().getLongOption(CmdParams.CHOOSE_MAG_IN_PAG));

diff --git a/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java b/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java
@@ -216,6 +216,8 @@ public void testGFCIWithContinuousData() throws IOException {
             "--algorithm", "gfci",
             "--test", "fisher-z-test",
             "--score", "sem-bic",
+            "--penaltyDiscount", "1.0",
+            "--structurePrior", "0.01",
             "--verbose",
             "--skip-latest",
             "--out", dirOut