Resolved conflict.

bd2kccd · Dec 11, 2022 · 5f1fce0 · 5f1fce0
2 parents 8cefd71 + 75d8525
commit 5f1fce0
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Showing 20 changed files with 266 additions and 215 deletions.
diff --git a/pom.xml b/pom.xml
@@ -3,14 +3,13 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-cmd</artifactId>
-    <version>1.4.1</version>
+    <version>1.4.2</version>
     <packaging>jar</packaging>
 
     <properties>
-        <java.version>11</java.version>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <maven.compiler.source>11</maven.compiler.source>
-        <maven.compiler.target>11</maven.compiler.target>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
     </properties>
 
     <dependencies>
@@ -46,7 +45,7 @@
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-engine</artifactId>
-            <version>5.8.2</version>
+            <version>5.9.1</version>
             <scope>test</scope>
         </dependency>
     </dependencies>
@@ -60,7 +59,7 @@
             </plugin>
             <plugin>
                 <artifactId>maven-resources-plugin</artifactId>
-                <version>3.2.0</version>
+                <version>3.3.0</version>
                 <executions>
                     <execution>
                         <id>copy-dist-resources</id>
@@ -83,7 +82,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>
-                <version>3.2.2</version>
+                <version>3.3.0</version>
                 <configuration>
                     <archive>
                         <manifest>
@@ -95,7 +94,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-assembly-plugin</artifactId>
-                <version>3.3.0</version>
+                <version>3.4.2</version>
                 <executions>
                     <execution>
                         <phase>package</phase>
@@ -134,7 +133,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
-                <version>3.4.0</version>
+                <version>3.4.1</version>
                 <configuration>
                     <javadocExecutable>/usr/bin/javadoc</javadocExecutable>
                     <!--<show>private</show>-->

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/Args.java b/src/main/java/edu/pitt/dbmi/causal/cmd/Args.java
@@ -72,7 +72,7 @@ public static String[] removeLongOption(String[] args, String option) {
             }
         }
 
-        return argsToKeep.toArray(String[]::new);
+        return argsToKeep.stream().toArray(String[]::new);
     }
 
     /**
@@ -143,7 +143,7 @@ public static String[] extractLongOptions(String[] args, Options options) {
             }
         });
 
-        return argsList.toArray(String[]::new);
+        return argsList.stream().toArray(String[]::new);
     }
 
     /**
@@ -179,7 +179,7 @@ public static String[] extractOptions(String[] args, Options options) {
             }
         });
 
-        return argsList.toArray(String[]::new);
+        return argsList.stream().toArray(String[]::new);
     }
 
     /**

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CausalCmdApplication.java
@@ -137,7 +137,7 @@ private static void runTetrad(CmdArgs cmdArgs) throws AlgorithmRunException, Val
             Files.deleteIfExists(outTxtFile);
         }
 
-        try ( PrintStream out = new PrintStream(new BufferedOutputStream(Files.newOutputStream(outTxtFile, StandardOpenOption.CREATE)), true)) {
+        try (PrintStream out = new PrintStream(new BufferedOutputStream(Files.newOutputStream(outTxtFile, StandardOpenOption.CREATE)), true)) {
             writeOutParameters(cmdArgs, out);
 
             if (!cmdArgs.isSkipValidation()) {
@@ -166,7 +166,7 @@ private static void runTetrad(CmdArgs cmdArgs) throws AlgorithmRunException, Val
 
                     Path outGraphFile = Paths.get(outDir, fileName);
                     if (Files.exists(outGraphFile)) {
-                        Files.deleteIfExists(outTxtFile);
+                        Files.deleteIfExists(outGraphFile);
                     }
 
                     GraphIO.writeAsJSON(graphs[i], outGraphFile);

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdArgs.java
@@ -79,7 +79,7 @@ public class CmdArgs {
      * by the data reader.
      */
     protected String commentMarker;
-    
+
     /**
      * Indicates whether the first line in the data file is a header.
      */
@@ -89,7 +89,7 @@ public class CmdArgs {
      * Type of data in the dataset.
      */
     protected DataType dataType;
-    
+
     /**
      * Data delimiter.
      */
@@ -99,12 +99,12 @@ public class CmdArgs {
      * Algorithm class.
      */
     protected Class algorithmClass;
-    
+
     /**
      * Score class.
      */
     protected Class scoreClass;
-    
+
     /**
      * Independence test class.
      */
@@ -119,14 +119,15 @@ public class CmdArgs {
      * Indicates whether or not to skip data validation.
      */
     protected boolean skipValidation;
-    
+
     /**
      * Indicates whether to output the search graph in JSON format.
      */
     protected boolean jsonGraph;
 
     /**
-     * Maximum number of threads can be used by algorithm, score, or independence test.
+     * Maximum number of threads can be used by algorithm, score, or
+     * independence test.
      */
     protected int numOfThreads;
 

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdOptions.java
@@ -54,7 +54,7 @@ private CmdOptions() {
     /**
      * Get an instance of the command-line options.
      *
-     * @return
+     * @return CmdOptions instance
      */
     public static CmdOptions getInstance() {
         if (instance == null) {
@@ -75,7 +75,7 @@ public static void clear() {
      * Get multi-character name options for a given name..
      *
      * @param param multi-character name
-     * @return
+     * @return command-line option
      */
     public Option getLongOption(String param) {
         return options.get(param);
@@ -165,12 +165,11 @@ public List<Option> getBaseOptions() {
         opts.add(options.get(CmdParams.DIR_OUT));
 
 //        opts.add(options.get(CmdParams.THREAD));
-
         // data validation options
         opts.add(options.get(CmdParams.SKIP_VALIDATION));
 
         opts.add(options.get(CmdParams.EXPERIMENTAL));
-        
+
         opts.add(options.get(CmdParams.DEFAULT));
 
         return opts;
@@ -250,7 +249,7 @@ private void addRequiredOptions() {
     /**
      * Get the application required options from the stored options.
      *
-     * @return
+     * @return required command-line options
      */
     public List<Option> getRequiredOptions() {
         return options.entrySet().stream()
@@ -262,7 +261,7 @@ public List<Option> getRequiredOptions() {
     /**
      * Get the names of all the datatypes.
      *
-     * @return
+     * @return datatype description
      */
     private String getDataTypeDesc() {
         return "Data type: " + DataTypes.getInstance().getNames().stream()
@@ -272,7 +271,7 @@ private String getDataTypeDesc() {
     /**
      * Get the names of all the delimiters.
      *
-     * @return
+     * @return names of delimiters
      */
     private String getDelimiterDesc() {
         return "Delimiter: " + Delimiters.getInstance().getNames().stream()
@@ -282,7 +281,7 @@ private String getDelimiterDesc() {
     /**
      * Get the names of all the scores.
      *
-     * @return
+     * @return description for score
      */
     private String getScoreDesc() {
         return "Score: " + TetradScores.getInstance().getCommands().stream()
@@ -292,7 +291,7 @@ private String getScoreDesc() {
     /**
      * Get the names of all the independence test.
      *
-     * @return
+     * @return description for test of independence
      */
     private String getIndependenceTestDesc() {
         return "Independence Test: " + TetradIndependenceTests.getInstance().getCommands().stream()
@@ -302,7 +301,7 @@ private String getIndependenceTestDesc() {
     /**
      * Get the names of all the algorithms.
      *
-     * @return
+     * @return description for algorithm
      */
     private String getAlgorithmDesc() {
         return "Algorithm: " + TetradAlgorithms.getInstance().getCommands().stream()

diff --git a/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java b/src/main/java/edu/pitt/dbmi/causal/cmd/CmdParams.java
@@ -78,7 +78,7 @@ public final class CmdParams {
     public static final String EXTRACT_STRUCT_MODEL = "extract-struct-model";
 
     public static final String EXPERIMENTAL = "experimental";
-    
+
     public static final String DEFAULT = "default";
 
     private CmdParams() {