Merge branch 'development'

Conflicts: pom.xml
bd2kccd · Oct 30, 2018 · 947bd8b · 947bd8b
2 parents f0339bb + e02a3f3
commit 947bd8b
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Showing 7 changed files with 58 additions and 117 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>0.3.1</version>
+    <version>0.4.1</version>
     <packaging>jar</packaging>
 
     <properties>
@@ -38,7 +38,7 @@
         <plugins>
             <plugin>
                 <artifactId>maven-resources-plugin</artifactId>
-                <version>3.0.2</version>
+                <version>3.1.0</version>
                 <executions>
                     <execution>
                         <id>copy-dist-resources</id>
@@ -61,7 +61,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.0.2</version>
+                <version>3.1.0</version>
                 <configuration>
                     <archive>
                         <manifest>
@@ -121,7 +121,7 @@
         <dependency>
             <groupId>edu.cmu</groupId>
             <artifactId>tetrad-lib</artifactId>
-            <version>6.4.0</version>
+            <version>6.6.0</version>
             <exclusions>
                 <exclusion>
                     <groupId>log4j</groupId>

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
@@ -57,6 +57,7 @@ public interface CmdParams {
     public static final String SCORE = "score";
 
     public static final String NUM_CATEGORIES = "numCategories";
+    public static final String TARGET_NAME = "targetName";
 
     public static final String THREAD = "thread";
 

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParser.java
@@ -31,6 +31,7 @@
 import edu.pitt.dbmi.causal.cmd.util.FileUtils;
 import edu.pitt.dbmi.causal.cmd.util.OptionFactory;
 import java.io.FileNotFoundException;
+import java.io.Serializable;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.HashMap;
@@ -249,7 +250,12 @@ private static ParseOptions getValidOptions(String[] args, Options options) thro
 
         // add Tetrad parameters
         params.forEach(param -> {
-            opts.addOption(CmdOptions.getInstance().getLongOption(param));
+            if (param.equals(CmdParams.TARGET_NAME)) {
+                // add required Tetrad parameters
+                opts.addOption(Option.builder().longOpt(CmdParams.TARGET_NAME).desc("Target variable.").hasArg().argName("string").required().build());
+            } else {
+                opts.addOption(CmdOptions.getInstance().getLongOption(param));
+            }
         });
 
         try {
@@ -357,7 +363,11 @@ private static Map<String, String> getValidParameters(CommandLine cmd, CmdArgs c
                 }
                 parameters.put(param, value);
             } else {
-                parameters.put(param, paramDesc.getDefaultValue().toString());
+                Serializable defaultValue = paramDesc.getDefaultValue();
+                String value = (defaultValue instanceof Boolean)
+                        ? Boolean.FALSE.toString()
+                        : defaultValue.toString();
+                parameters.put(param, value);
             }
         };
 

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradAlgorithms.java b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradAlgorithms.java
@@ -92,10 +92,11 @@ public String getName(Class clazz) {
                 : "";
     }
 
-    public String getDescription(Class clazz) {
-        return (clazz != null && clazz.isAnnotationPresent(Algorithm.class))
-                ? ((Algorithm) clazz.getAnnotation(Algorithm.class)).description()
-                : "";
-    }
+    // not used so commenting out as this is more tetrad gui
+//    public String getDescription(Class clazz) {
+//        return (clazz != null && clazz.isAnnotationPresent(Algorithm.class))
+//                ? ((Algorithm) clazz.getAnnotation(Algorithm.class)).description()
+//                : "";
+//    }
 
 }
diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradUtils.java b/src/main/java/edu/pitt/dbmi/causal/cmd/tetrad/TetradUtils.java
@@ -30,7 +30,6 @@
 import edu.pitt.dbmi.causal.cmd.CmdArgs;
 import edu.pitt.dbmi.causal.cmd.ValidationException;
 import edu.pitt.dbmi.causal.cmd.util.DateTime;
-import edu.pitt.dbmi.causal.cmd.util.FileIO;
 import edu.pitt.dbmi.data.Dataset;
 import edu.pitt.dbmi.data.reader.covariance.CovarianceDataReader;
 import edu.pitt.dbmi.data.reader.covariance.LowerCovarianceDataReader;
@@ -49,6 +48,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintStream;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.Collections;
 import java.util.HashSet;
@@ -57,6 +57,7 @@
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -172,18 +173,24 @@ public static IKnowledge readInKnowledge(CmdArgs cmdArgs, PrintStream out) throw
     }
 
     private static Set<String> getExcludeVariables(CmdArgs cmdArgs, PrintStream out) throws IOException {
-        Set<String> excludeVars;
-
         Path file = cmdArgs.getExcludeVariableFile();
         if (file == null) {
-            excludeVars = new HashSet<>();
+            return Collections.EMPTY_SET;
         } else {
+            Set<String> set = new HashSet<>();
+
             logStartReading(file, out);
-            excludeVars = FileIO.extractUniqueLine(cmdArgs.getExcludeVariableFile());
+            try (Stream<String> stream = Files.lines(file)) {
+                stream
+                        .map(e -> e.trim())
+                        .filter(e -> !e.isEmpty())
+                        .distinct()
+                        .collect(Collectors.toCollection(() -> set));
+            }
             logFinishReading(file, out);
-        }
 
-        return excludeVars;
+            return set;
+        }
     }
 
     public static List<DataModel> getDataModels(CmdArgs cmdArgs, PrintStream out) throws IOException {

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/util/FileIO.java b/src/main/java/edu/pitt/dbmi/causal/cmd/util/FileIO.java
diff --git a/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java b/src/test/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplicationTest.java
@@ -37,6 +37,24 @@ public class CausalCmdApplicationTest {
     public CausalCmdApplicationTest() {
     }
 
+    @Test
+    public void testMainFgesMb() throws IOException {
+        String contData = TestFiles.getInstance().getContinuousData().toString();
+        String dirOut = tmpFolder.newFolder("fges_mb").toString();
+        String[] args = {
+            "--dataset", contData,
+            "--delimiter", "tab",
+            "--data-type", "continuous",
+            "--algorithm", "fges-mb",
+            "--score", "sem-bic",
+            "--targetName", "X1",
+            "--verbose",
+            "--skip-latest",
+            "--out", dirOut
+        };
+        CausalCmdApplication.main(args);
+    }
+
     @Test
     public void testMainCovariance() throws IOException {
         String covarData = TestFiles.getInstance().getCovarianceData().toString();
@@ -60,8 +78,9 @@ public void testMainWithBootstrap() throws IOException {
         String contData = TestFiles.getInstance().getContinuousData().toString();
         String dirOut = tmpFolder.newFolder("gfci_bootstrap").toString();
         String[] args = {
-            "--bootstrapEnsemble", "1",
-            "--bootstrapSampleSize", "5",
+            "--resamplingEnsemble", "1",
+            "--numberResampling", "5",
+            "--resampleSize", "100",
             "--dataset", contData,
             "--delimiter", "tab",
             "--data-type", "continuous",