Merge pull request #166 from cmu-phil/cli-validations

Cli validations
cmu-phil · Mar 25, 2016 · 4ce0fed · 4ce0fed
2 parents 7cac6af + 5042ad5
commit 4ce0fed
Show file tree

Hide file tree

Showing 48 changed files with 16 additions and 11 deletions.
diff --git a/tetrad-cli/dist/README.txt → causal-cmd/dist/README.txt b/tetrad-cli/dist/README.txt → causal-cmd/dist/README.txt
diff --git a/tetrad-cli/dist/Retention.txt → causal-cmd/dist/Retention.txt b/tetrad-cli/dist/Retention.txt → causal-cmd/dist/Retention.txt
diff --git a/tetrad-cli/dist/tetrad-cli.cmd → causal-cmd/dist/tetrad-cli.cmd b/tetrad-cli/dist/tetrad-cli.cmd → causal-cmd/dist/tetrad-cli.cmd
diff --git a/tetrad-cli/dist/tetrad-cli.sh → causal-cmd/dist/tetrad-cli.sh b/tetrad-cli/dist/tetrad-cli.sh → causal-cmd/dist/tetrad-cli.sh
diff --git a/tetrad-cli/pom.xml → causal-cmd/pom.xml b/tetrad-cli/pom.xml → causal-cmd/pom.xml
@@ -7,7 +7,7 @@
         <artifactId>tetrad</artifactId>
         <version>5.3.0-SNAPSHOT</version>
     </parent>
-    <artifactId>tetrad-cli</artifactId>
+    <artifactId>causal-cmd</artifactId>
     <packaging>jar</packaging>
     <properties>
         <maven.compiler.source>1.7</maven.compiler.source>
@@ -107,7 +107,6 @@
             </plugin>
         </plugins>
     </build>
-
     <dependencies>
         <dependency>
             <groupId>edu.cmu</groupId>

diff --git a/tetrad-cli/src/assembly/distribution.xml → causal-cmd/src/assembly/distribution.xml b/tetrad-cli/src/assembly/distribution.xml → causal-cmd/src/assembly/distribution.xml
diff --git a/tetrad-cli/src/assembly/filter.properties → causal-cmd/src/assembly/filter.properties b/tetrad-cli/src/assembly/filter.properties → causal-cmd/src/assembly/filter.properties
diff --git a/...tetrad/cli/ExtendedCommandLineParser.java → ...tetrad/cli/ExtendedCommandLineParser.java b/...tetrad/cli/ExtendedCommandLineParser.java → ...tetrad/cli/ExtendedCommandLineParser.java
diff --git a/...java/edu/cmu/tetrad/cli/TetradCliApp.java → ...java/edu/cmu/tetrad/cli/TetradCliApp.java b/...java/edu/cmu/tetrad/cli/TetradCliApp.java → ...java/edu/cmu/tetrad/cli/TetradCliApp.java
@@ -27,6 +27,8 @@
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 /**
  *
@@ -36,6 +38,8 @@
  */
 public class TetradCliApp {
 
+    private static final Logger LOGGER = LoggerFactory.getLogger(TetradCliApp.class);
+
     private static final Options MAIN_OPTIONS = new Options();
 
     static {
@@ -81,10 +85,13 @@ private static void showVersion() {
             JarFile jarFile = new JarFile(TetradCliApp.class.getProtectionDomain().getCodeSource().getLocation().getPath(), true);
             Manifest manifest = jarFile.getManifest();
             Attributes attributes = manifest.getMainAttributes();
+            String artifactId = attributes.getValue("Implementation-Title");
             String version = attributes.getValue("Implementation-Version");
-            System.out.printf("Tetrad Command-line Interface (CLI) version %s%n", version);
+            System.out.printf("%s version: %s%n", artifactId, version);
         } catch (IOException exception) {
-            System.err.println("Unable to retrieve version number.");
+            String errMsg = "Unable to retrieve version number.";
+            System.err.println(errMsg);
+            LOGGER.error(errMsg, exception);
         }
     }
 
@@ -98,7 +105,7 @@ private static void showHelp() {
             String version = attributes.getValue("Implementation-Version");
             cmdLineSyntax += String.format("%s-%s.jar", artifactId, version);
         } catch (IOException exception) {
-            cmdLineSyntax += "tetrad-cli.jar";
+            cmdLineSyntax += "causal-cmd.jar";
         }
 
         HelpFormatter formatter = new HelpFormatter();

diff --git a/...u/tetrad/cli/data/AbstractDataReader.java → ...u/tetrad/cli/data/AbstractDataReader.java b/...u/tetrad/cli/data/AbstractDataReader.java → ...u/tetrad/cli/data/AbstractDataReader.java
diff --git a/...tetrad/cli/data/ContinuousDataReader.java → ...tetrad/cli/data/ContinuousDataReader.java b/...tetrad/cli/data/ContinuousDataReader.java → ...tetrad/cli/data/ContinuousDataReader.java
diff --git a/...u/cmu/tetrad/cli/data/DataSetFactory.java → ...u/cmu/tetrad/cli/data/DataSetFactory.java b/...u/cmu/tetrad/cli/data/DataSetFactory.java → ...u/cmu/tetrad/cli/data/DataSetFactory.java
diff --git a/...va/edu/cmu/tetrad/cli/data/DataSetIO.java → ...va/edu/cmu/tetrad/cli/data/DataSetIO.java b/...va/edu/cmu/tetrad/cli/data/DataSetIO.java → ...va/edu/cmu/tetrad/cli/data/DataSetIO.java
diff --git a/...mu/tetrad/cli/data/IKnowledgeFactory.java → ...mu/tetrad/cli/data/IKnowledgeFactory.java b/...mu/tetrad/cli/data/IKnowledgeFactory.java → ...mu/tetrad/cli/data/IKnowledgeFactory.java
diff --git a/...cli/data/TabularContinuousDataReader.java → ...cli/data/TabularContinuousDataReader.java b/...cli/data/TabularContinuousDataReader.java → ...cli/data/TabularContinuousDataReader.java
diff --git a/...du/cmu/tetrad/cli/graph/GraphFactory.java → ...du/cmu/tetrad/cli/graph/GraphFactory.java b/...du/cmu/tetrad/cli/graph/GraphFactory.java → ...du/cmu/tetrad/cli/graph/GraphFactory.java
diff --git a/...ava/edu/cmu/tetrad/cli/graph/GraphIO.java → ...ava/edu/cmu/tetrad/cli/graph/GraphIO.java b/...ava/edu/cmu/tetrad/cli/graph/GraphIO.java → ...ava/edu/cmu/tetrad/cli/graph/GraphIO.java
diff --git a/...ava/edu/cmu/tetrad/cli/search/FgsCli.java → ...ava/edu/cmu/tetrad/cli/search/FgsCli.java b/...ava/edu/cmu/tetrad/cli/search/FgsCli.java → ...ava/edu/cmu/tetrad/cli/search/FgsCli.java
@@ -268,8 +268,8 @@ private static void printArgs(PrintStream writer) {
             formatter.format("data=%s,", dataFile.getFileName());
         }
         if (variableFile != null) {
-            writer.printf("variables = %s%n", variableFile.getFileName());
-            formatter.format("variables=%s,", variableFile.getFileName());
+            writer.printf("excluded variables = %s%n", variableFile.getFileName());
+            formatter.format("excluded variables=%s,", variableFile.getFileName());
         }
         if (knowledgeFile != null) {
             writer.printf("knowledge = %s%n", knowledgeFile.getFileName());

diff --git a/...in/java/edu/cmu/tetrad/cli/util/Args.java → ...in/java/edu/cmu/tetrad/cli/util/Args.java b/...in/java/edu/cmu/tetrad/cli/util/Args.java → ...in/java/edu/cmu/tetrad/cli/util/Args.java
diff --git a/...ava/edu/cmu/tetrad/cli/util/DateTime.java → ...ava/edu/cmu/tetrad/cli/util/DateTime.java b/...ava/edu/cmu/tetrad/cli/util/DateTime.java → ...ava/edu/cmu/tetrad/cli/util/DateTime.java
diff --git a/.../java/edu/cmu/tetrad/cli/util/FileIO.java → .../java/edu/cmu/tetrad/cli/util/FileIO.java b/.../java/edu/cmu/tetrad/cli/util/FileIO.java → .../java/edu/cmu/tetrad/cli/util/FileIO.java
diff --git a/...mu/tetrad/cli/util/GraphmlSerializer.java → ...mu/tetrad/cli/util/GraphmlSerializer.java b/...mu/tetrad/cli/util/GraphmlSerializer.java → ...mu/tetrad/cli/util/GraphmlSerializer.java
diff --git a/...ava/edu/cmu/tetrad/cli/util/XmlPrint.java → ...ava/edu/cmu/tetrad/cli/util/XmlPrint.java b/...ava/edu/cmu/tetrad/cli/util/XmlPrint.java → ...ava/edu/cmu/tetrad/cli/util/XmlPrint.java
diff --git a/...tetrad/cli/validation/DataValidation.java → ...tetrad/cli/validation/DataValidation.java b/...tetrad/cli/validation/DataValidation.java → ...tetrad/cli/validation/DataValidation.java
diff --git a/...etrad/cli/validation/NonZeroVariance.java → ...etrad/cli/validation/NonZeroVariance.java b/...etrad/cli/validation/NonZeroVariance.java → ...etrad/cli/validation/NonZeroVariance.java
diff --git a/...cli/validation/TabularContinuousData.java → ...cli/validation/TabularContinuousData.java b/...cli/validation/TabularContinuousData.java → ...cli/validation/TabularContinuousData.java
diff --git a/...d/cli/validation/UniqueVariableNames.java → ...d/cli/validation/UniqueVariableNames.java b/...d/cli/validation/UniqueVariableNames.java → ...d/cli/validation/UniqueVariableNames.java
diff --git a/...d-cli/src/main/resources/log4j.properties → ...l-cmd/src/main/resources/log4j.properties b/...d-cli/src/main/resources/log4j.properties → ...l-cmd/src/main/resources/log4j.properties
@@ -1,6 +1,6 @@
 log4j.rootLogger=INFO,file
 
-log4j.appender.file.File=tetrad-cli.log
+log4j.appender.file.File=causal-cmd.log
 log4j.appender.file=org.apache.log4j.RollingFileAppender
 log4j.appender.file.MaxFileSize=10MB
 log4j.appender.file.MaxBackupIndex=10

diff --git a/tetrad-cli/src/main/xsd/graphml.xsd → causal-cmd/src/main/xsd/graphml.xsd b/tetrad-cli/src/main/xsd/graphml.xsd → causal-cmd/src/main/xsd/graphml.xsd
diff --git a/...st/java/edu/cmu/tetrad/cli/FilePrint.java → ...st/java/edu/cmu/tetrad/cli/FilePrint.java b/...st/java/edu/cmu/tetrad/cli/FilePrint.java → ...st/java/edu/cmu/tetrad/cli/FilePrint.java
diff --git a/...data/TabularContinuousDataReaderTest.java → ...data/TabularContinuousDataReaderTest.java b/...data/TabularContinuousDataReaderTest.java → ...data/TabularContinuousDataReaderTest.java
diff --git a/.../cmu/tetrad/cli/search/FgsApiExample.java → .../cmu/tetrad/cli/search/FgsApiExample.java b/.../cmu/tetrad/cli/search/FgsApiExample.java → .../cmu/tetrad/cli/search/FgsApiExample.java
diff --git a/...edu/cmu/tetrad/cli/search/FgsCliTest.java → ...edu/cmu/tetrad/cli/search/FgsCliTest.java b/...edu/cmu/tetrad/cli/search/FgsCliTest.java → ...edu/cmu/tetrad/cli/search/FgsCliTest.java
diff --git a/...d/cli/validation/NonZeroVarianceTest.java → ...d/cli/validation/NonZeroVarianceTest.java b/...d/cli/validation/NonZeroVarianceTest.java → ...d/cli/validation/NonZeroVarianceTest.java
diff --git a/...validation/TabularContinuousDataTest.java → ...validation/TabularContinuousDataTest.java b/...validation/TabularContinuousDataTest.java → ...validation/TabularContinuousDataTest.java
diff --git a/...i/validation/UniqueVariableNamesTest.java → ...i/validation/UniqueVariableNamesTest.java b/...i/validation/UniqueVariableNamesTest.java → ...i/validation/UniqueVariableNamesTest.java
diff --git a/...a/diff_delim/sim_data_20vars_100cases.csv → ...a/diff_delim/sim_data_20vars_100cases.csv b/...a/diff_delim/sim_data_20vars_100cases.csv → ...a/diff_delim/sim_data_20vars_100cases.csv
diff --git a/...a/diff_delim/sim_data_20vars_100cases.txt → ...a/diff_delim/sim_data_20vars_100cases.txt b/...a/diff_delim/sim_data_20vars_100cases.txt → ...a/diff_delim/sim_data_20vars_100cases.txt
diff --git a/...s_format/dos_sim_data_20vars_100cases.csv → ...s_format/dos_sim_data_20vars_100cases.csv b/...s_format/dos_sim_data_20vars_100cases.csv → ...s_format/dos_sim_data_20vars_100cases.csv
diff --git a/...s_format/mac_sim_data_20vars_100cases.csv → ...s_format/mac_sim_data_20vars_100cases.csv b/...s_format/mac_sim_data_20vars_100cases.csv → ...s_format/mac_sim_data_20vars_100cases.csv
diff --git a/..._format/unix_sim_data_20vars_100cases.csv → ..._format/unix_sim_data_20vars_100cases.csv b/..._format/unix_sim_data_20vars_100cases.csv → ..._format/unix_sim_data_20vars_100cases.csv
diff --git a/...ssing_values/sim_data_20vars_100cases.csv → ...ssing_values/sim_data_20vars_100cases.csv b/...ssing_values/sim_data_20vars_100cases.csv → ...ssing_values/sim_data_20vars_100cases.csv
diff --git a/...me_and_value/sim_data_20vars_100cases.csv → ...me_and_value/sim_data_20vars_100cases.csv b/...me_and_value/sim_data_20vars_100cases.csv → ...me_and_value/sim_data_20vars_100cases.csv
diff --git a/...ue_var_names/sim_data_20vars_100cases.csv → ...ue_var_names/sim_data_20vars_100cases.csv b/...ue_var_names/sim_data_20vars_100cases.csv → ...ue_var_names/sim_data_20vars_100cases.csv
diff --git a/..._unique_vars/sim_data_20vars_100cases.csv → ..._unique_vars/sim_data_20vars_100cases.csv b/..._unique_vars/sim_data_20vars_100cases.csv → ..._unique_vars/sim_data_20vars_100cases.csv
diff --git a/tetrad-cli/test/data/variables.txt → causal-cmd/test/data/variables.txt b/tetrad-cli/test/data/variables.txt → causal-cmd/test/data/variables.txt
diff --git a/...ariance_vars/sim_data_20vars_100cases.csv → ...ariance_vars/sim_data_20vars_100cases.csv b/...ariance_vars/sim_data_20vars_100cases.csv → ...ariance_vars/sim_data_20vars_100cases.csv
diff --git a/pom.xml b/pom.xml
@@ -1,8 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project xmlns="http://maven.apache.org/POM/4.0.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 
-http://maven.apache.org/maven-v4_0_0.xsd">
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <groupId>edu.cmu</groupId>
     <artifactId>tetrad</artifactId>
@@ -12,8 +11,8 @@ http://maven.apache.org/maven-v4_0_0.xsd">
     <name>Tetrad Project</name>
     <modules>
         <module>tetrad-gui</module>
-        <module>tetrad-cli</module>
         <module>tetrad-lib</module>
+        <module>causal-cmd</module>
     </modules>
 
     <licenses>