fixing commandline invocation in case of erroneous parameters

ratschlab · Oct 6, 2021 · ff19dca · ff19dca
1 parent ddf3e5d
commit ff19dca
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Showing 9 changed files with 37 additions and 11 deletions.
diff --git a/deidentifier-pipeline/src/main/java/org/ratschlab/DeidCmd.java b/deidentifier-pipeline/src/main/java/org/ratschlab/DeidCmd.java
@@ -0,0 +1,11 @@
+package org.ratschlab;
+
+import java.util.concurrent.Callable;
+
+public class DeidCmd implements Callable<Integer> {
+    @Override
+    public Integer call() {
+        org.ratschlab.util.Utils.tieSystemOutAndErrToLog();
+        return null;
+    }
+}
diff --git a/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/AnnotationCmd.java b/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/AnnotationCmd.java
@@ -29,7 +29,7 @@
 import java.util.stream.Stream;
 
 @CommandLine.Command(description = "Annotate Corpus", name = "annotate")
-public class AnnotationCmd extends DbCommands implements Callable<Integer> {
+public class AnnotationCmd extends DbCommands {
     private static final Logger log = LoggerFactory.getLogger(AnnotationCmd.class);
 
     @CommandLine.Option(names = {"-i"}, description = "Input corpus dir")
@@ -106,6 +106,8 @@ private PipelineWorkflow<?> readFromFiles(List<WorkflowConcern> concerns, Serial
 
     @Override
     public Integer call() {
+        super.call();
+
         if(corpusInputDirPath == null && databaseConfigPath == null) {
             System.err.println("Need at least -i or -d");
             return 1;

diff --git a/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/DeidMain.java b/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/DeidMain.java
@@ -27,8 +27,10 @@ public Integer call() {
     }
 
     public static void main(String[] args) {
-        org.ratschlab.util.Utils.tieSystemOutAndErrToLog();
-        int exitCode = CommandLine.call(new DeidMain(), args);
+        Integer exitCode = CommandLine.call(new DeidMain(), args);
+        if(exitCode == null) {
+            System.exit(2);
+        }
         System.exit(exitCode);
     }
 }
diff --git a/...ipeline/src/main/java/org/ratschlab/deidentifier/pipelines/testing/PipelineTesterCmd.java b/...ipeline/src/main/java/org/ratschlab/deidentifier/pipelines/testing/PipelineTesterCmd.java
@@ -2,16 +2,16 @@
 
 import gate.Gate;
 import gate.util.GateException;
+import org.ratschlab.DeidCmd;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import picocli.CommandLine;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.concurrent.Callable;
 
 @CommandLine.Command(description = "Tests a pipeline", name = "test")
-public class PipelineTesterCmd implements Callable<Integer> {
+public class PipelineTesterCmd extends DeidCmd {
     private static final Logger log = LoggerFactory.getLogger(PipelineTesterCmd.class);
 
     @CommandLine.Parameters(index = "0", description = "Pipeline Configuration File")
@@ -29,6 +29,8 @@ public static void main(String[] args) {
 
     @Override
     public Integer call() {
+        super.call();
+
         try {
             Gate.init();
 

diff --git a/...ntifier-pipeline/src/main/java/org/ratschlab/deidentifier/sources/ConversionCheckCmd.java b/...ntifier-pipeline/src/main/java/org/ratschlab/deidentifier/sources/ConversionCheckCmd.java
@@ -21,7 +21,7 @@
 import java.util.stream.Stream;
 
 @CommandLine.Command(mixinStandardHelpOptions = true, description = "Roundtrip test between JSON <--> GATE format", name = "conversioncheck")
-public class ConversionCheckCmd extends DbCommands implements Callable<Integer> {
+public class ConversionCheckCmd extends DbCommands {
 
     private static final Logger log = LoggerFactory.getLogger(ConversionCheckCmd.class);
 
@@ -30,6 +30,8 @@ public class ConversionCheckCmd extends DbCommands implements Callable<Integer>
 
     @Override
     public Integer call() {
+        super.call();
+
         try {
             Gate.init();
 

diff --git a/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/sources/ConversionCmd.java b/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/sources/ConversionCmd.java
@@ -4,6 +4,7 @@
 import gate.corpora.DocumentJsonUtils;
 import gate.util.GateException;
 import org.apache.commons.lang.NotImplementedException;
+import org.ratschlab.DeidCmd;
 import org.ratschlab.gate.GateTools;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -17,7 +18,7 @@
 import java.util.stream.Stream;
 
 @CommandLine.Command(description = "Convert reports into different formats", name = "convert")
-public class ConversionCmd implements Callable<Integer> {
+public class ConversionCmd extends DeidCmd {
     private static final Logger log = LoggerFactory.getLogger(ConversionCmd.class);
 
     @CommandLine.Option(names = {"-i"}, description = "Input dir", required = true)
@@ -90,6 +91,7 @@ protected static void convertGateCorpusToGateJson(File inputDir, File outputDir)
 
     @Override
     public Integer call() {
+        super.call();
         try {
             Gate.init();
 

diff --git a/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/sources/ImportCmd.java b/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/sources/ImportCmd.java
@@ -32,7 +32,7 @@
 import java.util.stream.Stream;
 
 @CommandLine.Command(description = "Import reports from database", name = "import")
-public class ImportCmd extends DbCommands implements Callable<Integer> {
+public class ImportCmd extends DbCommands {
 
     private static final Logger log = LoggerFactory.getLogger(ImportCmd.class);
 
@@ -46,6 +46,8 @@ public static void main(String[] args) {
 
     @Override
     public Integer call() {
+        super.call();
+
         try {
             Gate.init();
 

diff --git a/...ifier-pipeline/src/main/java/org/ratschlab/deidentifier/substitution/SubstitutionCmd.java b/...ifier-pipeline/src/main/java/org/ratschlab/deidentifier/substitution/SubstitutionCmd.java
@@ -4,6 +4,7 @@
 import gate.*;
 import gate.creole.SerialAnalyserController;
 import gate.util.GateException;
+import org.ratschlab.DeidCmd;
 import org.ratschlab.deidentifier.annotation.features.FeatureKeysDate;
 import org.ratschlab.deidentifier.pipelines.PipelineFactory;
 import org.ratschlab.deidentifier.sources.KisimFormat;
@@ -30,7 +31,7 @@
 import java.util.stream.Stream;
 
 @CommandLine.Command(description = "Apply Substitution to Annotated Corpus", name = "substitute")
-public class SubstitutionCmd implements Callable<Integer> {
+public class SubstitutionCmd extends DeidCmd {
     private static final Logger log = LoggerFactory.getLogger(SubstitutionCmd.class);
 
     @CommandLine.Parameters(index = "0", description = "Corpus Dir")
@@ -102,7 +103,8 @@ public static Set<String> loadDocTypeSet(File path) throws IOException {
 
     @Override
     public Integer call() {
-        // TODO: really?
+        super.call();
+
         if(outputDir != null && outputDir.exists()) {
             try {
                 Files.delete(outputDir.toPath());

diff --git a/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/utils/DbCommands.java b/deidentifier-pipeline/src/main/java/org/ratschlab/deidentifier/utils/DbCommands.java
@@ -1,10 +1,11 @@
 package org.ratschlab.deidentifier.utils;
 
+import org.ratschlab.DeidCmd;
 import picocli.CommandLine;
 
 import java.util.stream.Stream;
 
-public class DbCommands {
+public class DbCommands extends DeidCmd {
     @CommandLine.Option(names = {"-d"}, description = "DB config path")
     protected String databaseConfigPath = "";