Merge pull request #1580 from Mailaender/process-builder-parameters

Fix invalid parameters for process builder
eclipse · Dec 11, 2023 · fbd4705 · fbd4705
2 parents 33bbed5 + fa71136
commit fbd4705
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Showing 27 changed files with 181 additions and 132 deletions.
diff --git a/...se/chemclipse/chromatogram/msd/peak/detector/supplier/amdis/runtime/LinuxWineSupport.java b/...se/chemclipse/chromatogram/msd/peak/detector/supplier/amdis/runtime/LinuxWineSupport.java
@@ -7,12 +7,13 @@
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.msd.peak.detector.supplier.amdis.runtime;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.util.List;
 import java.util.Map;
 
 import org.eclipse.chemclipse.support.runtime.AbstractLinuxWineSupport;
@@ -21,9 +22,9 @@ public class LinuxWineSupport extends AbstractLinuxWineSupport implements IExten
 
  private IAmdisSupport amdisSupport;
 
- public LinuxWineSupport(String application, String parameter) throws FileNotFoundException {
+ public LinuxWineSupport(String application, List<String> parameters) throws FileNotFoundException {
 
- super(application, parameter);
+ super(application, parameters);
  amdisSupport = new AmdisSupport(this);
  }
 

diff --git a/...ipse/chemclipse/chromatogram/msd/peak/detector/supplier/amdis/runtime/MacWineSupport.java b/...ipse/chemclipse/chromatogram/msd/peak/detector/supplier/amdis/runtime/MacWineSupport.java
@@ -1,17 +1,18 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2018 Lablicate GmbH.
+ * Copyright (c) 2014, 2023 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0 which accompanies this distribution,
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.msd.peak.detector.supplier.amdis.runtime;
 
 import java.io.FileNotFoundException;
+import java.util.List;
 
 import org.eclipse.chemclipse.chromatogram.msd.peak.detector.supplier.amdis.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.support.runtime.AbstractMacWineSupport;
@@ -20,8 +21,9 @@ public class MacWineSupport extends AbstractMacWineSupport implements IExtendedR
 
  private IAmdisSupport amdisSupport;
 
- public MacWineSupport(String application, String parameter) throws FileNotFoundException {
- super(application, parameter, PreferenceSupplier.getMacWineBinary());
+ public MacWineSupport(String application, List<String> parameters) throws FileNotFoundException {
+
+ super(application, parameters, PreferenceSupplier.getMacWineBinary());
  amdisSupport = new AmdisSupport(this);
  }
 

diff --git a/...emclipse/chromatogram/msd/peak/detector/supplier/amdis/runtime/RuntimeSupportFactory.java b/...emclipse/chromatogram/msd/peak/detector/supplier/amdis/runtime/RuntimeSupportFactory.java
@@ -1,17 +1,19 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2018 Lablicate GmbH.
+ * Copyright (c) 2014, 2023 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0 which accompanies this distribution,
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.msd.peak.detector.supplier.amdis.runtime;
 
 import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.eclipse.chemclipse.support.settings.OperatingSystemUtils;
 
@@ -20,16 +22,18 @@ public class RuntimeSupportFactory {
  public static IExtendedRuntimeSupport getRuntimeSupport(String application, String chromatogram) throws FileNotFoundException {
 
  IExtendedRuntimeSupport runtimeSupport;
- String parameter = chromatogram + " " + IAmdisSupport.PARAMETER;
+ List<String> parameters = new ArrayList<>();
+ parameters.add(chromatogram);
+ parameters.add(IAmdisSupport.PARAMETER);
  if(OperatingSystemUtils.isWindows()) {
- runtimeSupport = new WindowsSupport(application, parameter);
+ runtimeSupport = new WindowsSupport(application, parameters);
  } else if(OperatingSystemUtils.isMac()) {
- runtimeSupport = new MacWineSupport(application, parameter);
+ runtimeSupport = new MacWineSupport(application, parameters);
  } else {
  /*
  * wine AMDIS32\$.exe C:\\tmp\\C2.CDF /S
  */
- runtimeSupport = new LinuxWineSupport(application, parameter);
+ runtimeSupport = new LinuxWineSupport(application, parameters);
  }
  return runtimeSupport;
  }

diff --git a/...ipse/chemclipse/chromatogram/msd/peak/detector/supplier/amdis/runtime/WindowsSupport.java b/...ipse/chemclipse/chromatogram/msd/peak/detector/supplier/amdis/runtime/WindowsSupport.java
@@ -7,22 +7,23 @@
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  *******************************************************************************/
 package org.eclipse.chemclipse.chromatogram.msd.peak.detector.supplier.amdis.runtime;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.util.List;
 
 import org.eclipse.chemclipse.support.runtime.AbstractWindowsSupport;
 
 public class WindowsSupport extends AbstractWindowsSupport implements IExtendedRuntimeSupport {
 
  private IAmdisSupport amdisSupport;
 
- public WindowsSupport(String application, String parameter) throws FileNotFoundException {
+ public WindowsSupport(String application, List<String> parameters) throws FileNotFoundException {
 
- super(application, parameter);
+ super(application, parameters);
  amdisSupport = new AmdisSupport(this);
  }
 

diff --git a/.../org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/IExtendedRuntimeSupport.java b/.../org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/IExtendedRuntimeSupport.java
@@ -1,16 +1,18 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2020 Lablicate GmbH.
+ * Copyright (c) 2014, 2023 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0 which accompanies this distribution,
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.identifier.supplier.nist.runtime;
 
+import java.util.List;
+
 import org.eclipse.chemclipse.support.runtime.IRuntimeSupport;
 
 public interface IExtendedRuntimeSupport extends IRuntimeSupport {
@@ -30,7 +32,7 @@ public interface IExtendedRuntimeSupport extends IRuntimeSupport {
  */
  default boolean isBatchModus() {
 
- String parameter = getParameter();
+ List<String> parameter = getParameters();
  if(parameter != null) {
  return parameter.contains(INistSupport.PAR2);
  }

diff --git a/...er.nist/src/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/INistSupport.java b/...er.nist/src/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/INistSupport.java
@@ -1,13 +1,13 @@
 /*******************************************************************************
- * Copyright (c) 2008, 2022 Lablicate GmbH.
+ * Copyright (c) 2008, 2023 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0 which accompanies this distribution,
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.identifier.supplier.nist.runtime;
 
@@ -27,8 +27,6 @@ public interface INistSupport {
  */
  String PAR2 = "/PAR=2";
  String INSTRUMENT = "/INSTRUMENT";
- String PARAMETER_BACKGROUND = INSTRUMENT + " " + PAR2;
- String PARAMETER_FOREGROUND = INSTRUMENT;
  /*
  * The path is NIST library specific.
  */

diff --git a/...ist/src/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/LinuxWineSupport.java b/...ist/src/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/LinuxWineSupport.java
@@ -7,14 +7,15 @@
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  * Christoph Läubrich - using a path instead of a string
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.identifier.supplier.nist.runtime;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.util.List;
 import java.util.Map;
 
 import org.eclipse.chemclipse.msd.identifier.supplier.nist.preferences.PreferenceSupplier;
@@ -24,9 +25,9 @@ public class LinuxWineSupport extends AbstractLinuxWineSupport implements IExten
 
  private final INistSupport nistSupport;
 
- public LinuxWineSupport(File applicationFolder, String parameter) throws FileNotFoundException {
+ public LinuxWineSupport(File applicationFolder, List<String> parameters) throws FileNotFoundException {
 
- super(PreferenceSupplier.getNistExecutable(applicationFolder).getAbsolutePath(), parameter);
+ super(PreferenceSupplier.getNistExecutable(applicationFolder).getAbsolutePath(), parameters);
  nistSupport = new NistSupport(this);
  }
 

diff --git a/....nist/src/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/MacWineSupport.java b/....nist/src/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/MacWineSupport.java
@@ -1,19 +1,20 @@
 /*******************************************************************************
- * Copyright (c) 2011, 2019 Lablicate GmbH.
+ * Copyright (c) 2011, 2023 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0 which accompanies this distribution,
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  * Christoph Läubrich - using a path instead of a string
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.identifier.supplier.nist.runtime;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.util.List;
 
 import org.eclipse.chemclipse.msd.identifier.supplier.nist.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.support.runtime.AbstractMacWineSupport;
@@ -22,8 +23,9 @@ public class MacWineSupport extends AbstractMacWineSupport implements IExtendedR
 
  private final INistSupport nistSupport;
 
- public MacWineSupport(File applicationFolder, String parameter) throws FileNotFoundException {
- super(PreferenceSupplier.getNistExecutable(applicationFolder).getAbsolutePath(), parameter, PreferenceSupplier.getMacWineBinary());
+ public MacWineSupport(File applicationFolder, List<String> parameters) throws FileNotFoundException {
+
+ super(PreferenceSupplier.getNistExecutable(applicationFolder).getAbsolutePath(), parameters, PreferenceSupplier.getMacWineBinary());
  nistSupport = new NistSupport(this);
  }
 

diff --git a/...rc/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/RuntimeSupportFactory.java b/...rc/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/RuntimeSupportFactory.java
@@ -1,19 +1,21 @@
 /*******************************************************************************
- * Copyright (c) 2012, 2020 Lablicate GmbH.
+ * Copyright (c) 2012, 2023 Lablicate GmbH.
  * 
  * All rights reserved.
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Public License v1.0 which accompanies this distribution,
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  * Christoph Läubrich - using a path instead of a string
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.identifier.supplier.nist.runtime;
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.eclipse.chemclipse.support.settings.OperatingSystemUtils;
 
@@ -43,14 +45,17 @@ public static IExtendedRuntimeSupport getRuntimeSupport(File applicationFolder)
  public static IExtendedRuntimeSupport getRuntimeSupport(File applicationFolder, boolean batchModus) throws FileNotFoundException {
 
  IExtendedRuntimeSupport runtimeSupport;
- String parameter = batchModus ? INistSupport.PARAMETER_BACKGROUND : INistSupport.PARAMETER_FOREGROUND;
- //
+ List<String> parameters = new ArrayList<>();
+ parameters.add(INistSupport.INSTRUMENT);
+ if(batchModus) {
+ parameters.add(INistSupport.PAR2);
+ }
  if(OperatingSystemUtils.isWindows()) {
- runtimeSupport = new WindowsSupport(applicationFolder, parameter);
+ runtimeSupport = new WindowsSupport(applicationFolder, parameters);
  } else if(OperatingSystemUtils.isMac()) {
- runtimeSupport = new MacWineSupport(applicationFolder, parameter);
+ runtimeSupport = new MacWineSupport(applicationFolder, parameters);
  } else {
- runtimeSupport = new LinuxWineSupport(applicationFolder, parameter);
+ runtimeSupport = new LinuxWineSupport(applicationFolder, parameters);
  }
  return runtimeSupport;
  }

diff --git a/....nist/src/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/WindowsSupport.java b/....nist/src/org/eclipse/chemclipse/msd/identifier/supplier/nist/runtime/WindowsSupport.java
@@ -7,14 +7,15 @@
  * and is available at http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  * Christoph Läubrich - using a path instead of a string
  *******************************************************************************/
 package org.eclipse.chemclipse.msd.identifier.supplier.nist.runtime;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.util.List;
 
 import org.eclipse.chemclipse.msd.identifier.supplier.nist.preferences.PreferenceSupplier;
 import org.eclipse.chemclipse.support.runtime.AbstractWindowsSupport;
@@ -23,9 +24,9 @@ public class WindowsSupport extends AbstractWindowsSupport implements IExtendedR
 
  private final INistSupport nistSupport;
 
- public WindowsSupport(File applicationFolder, String parameter) throws FileNotFoundException {
+ public WindowsSupport(File applicationFolder, List<String> parameters) throws FileNotFoundException {
 
- super(PreferenceSupplier.getNistExecutable(applicationFolder).getAbsolutePath(), parameter);
+ super(PreferenceSupplier.getNistExecutable(applicationFolder).getAbsolutePath(), parameters);
  nistSupport = new NistSupport(this);
  }
 

diff --git a/...emclipse.support/src/org/eclipse/chemclipse/support/runtime/AbstractLinuxWineSupport.java b/...emclipse.support/src/org/eclipse/chemclipse/support/runtime/AbstractLinuxWineSupport.java
@@ -7,12 +7,14 @@
  * http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  *******************************************************************************/
 package org.eclipse.chemclipse.support.runtime;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
 import java.util.Map;
 
 public abstract class AbstractLinuxWineSupport extends AbstractWineRuntimeSupport implements IWineRuntimeSupport {
@@ -24,7 +26,7 @@ public abstract class AbstractLinuxWineSupport extends AbstractWineRuntimeSuppor
  * @param application
  * @param parameter
  */
- protected AbstractLinuxWineSupport(String application, String parameter) throws FileNotFoundException {
+ protected AbstractLinuxWineSupport(String application, List<String> parameter) throws FileNotFoundException {
 
  super(application, parameter);
  }
@@ -40,7 +42,12 @@ private ProcessBuilder getRunCommand() {
  /*
  * "env WINEPREFIX=/home/chemclipse/.wine wine start C:\\programme\\nist\\MSSEARCH\\nistms$.exe /INSTRUMENT /PAR=2"
  */
- ProcessBuilder processBuilder = new ProcessBuilder("wine", "start", getWineApplication(), getParameter());
+ List<String> commands = new ArrayList<>();
+ commands.add("wine");
+ commands.add("start");
+ commands.add(getWineApplication());
+ commands.addAll(getParameters());
+ ProcessBuilder processBuilder = new ProcessBuilder(commands);
  Map<String, String> environment = processBuilder.environment();
  environment.put("WINEPREFIX", getWineEnvironment());
  return processBuilder;

diff --git a/...chemclipse.support/src/org/eclipse/chemclipse/support/runtime/AbstractMacWineSupport.java b/...chemclipse.support/src/org/eclipse/chemclipse/support/runtime/AbstractMacWineSupport.java
@@ -7,12 +7,13 @@
  * http://www.eclipse.org/legal/epl-v10.html
  * 
  * Contributors:
- * Dr. Philip Wenig - initial API and implementation
+ * Philip Wenig - initial API and implementation
  *******************************************************************************/
 package org.eclipse.chemclipse.support.runtime;
 
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.util.List;
 
 public abstract class AbstractMacWineSupport extends AbstractWineRuntimeSupport implements IWineRuntimeSupport {
 
@@ -27,9 +28,9 @@ public abstract class AbstractMacWineSupport extends AbstractWineRuntimeSupport
  * @param macWineBinary
  * (e.g. "/Applications/Wine.app")
  */
- protected AbstractMacWineSupport(String application, String parameter, String macWineBinary) throws FileNotFoundException {
+ protected AbstractMacWineSupport(String application, List<String> parameters, String macWineBinary) throws FileNotFoundException {
 
- super(application, parameter);
+ super(application, parameters);
  this.macWineBinary = macWineBinary;
  }