Bugfix/relativepaths

rabix-bindings-cwl/src/main/java/org/rabix/bindings/cwl/helper/CWLFileValueHelper.java

@@ -383,17 +383,23 @@ public static void buildMissingInfo(Object value, HashAlgorithm alg, Path workDi
         return;
       }
     }
-    
+
     if (location == null) {
       actual = workDir.resolve(path);
       location = actual.toUri().toString();
     } else {
-      actual = Paths.get(URI.create(location));
-    }
-    if(!Paths.get(path).isAbsolute()){
-      path=workDir.resolve(path).toAbsolutePath().toString();
+      URI temp = URI.create(location);
+      if (temp.getScheme() != null) {
+        actual = Paths.get(temp);
+      } else {
+        actual = workDir.resolve(path);
+      }
     }
 
+    if (!Paths.get(path).isAbsolute()) {
+      path = workDir.resolve(path).toAbsolutePath().toString();
+    }
+
     String name = getName(value);
     if (name == null) {
       setNames(actual, value);
@@ -402,10 +408,10 @@ public static void buildMissingInfo(Object value, HashAlgorithm alg, Path workDi
         path = Paths.get(path).resolveSibling(name).toString();
       }
     }
-    
+
     setPath(path, value);
     setLocation(location, value);
-    
+
     if (getSize(value) == null)
       setSize(Files.size(actual), value);
 

rabix-bindings-cwl/src/main/java/org/rabix/bindings/cwl/processor/callback/CWLPortProcessorHelper.java

@@ -64,19 +64,12 @@ public Map<String, Object> updateOutputFiles(Map<String, Object> outputs, FileTr
 
   public Map<String, Object> setFileProperties(Map<String, Object> inputs) throws CWLPortProcessorException {
     try {
-      return portProcessor.processInputs(inputs, new CWLFilePropertiesProcessorCallback(Paths.get(portProcessor.getJob().getApp().getAppFileLocation())));
+      String appFileLocation = portProcessor.getJob().getApp().getAppFileLocation();
+      return portProcessor.processInputs(inputs, new CWLFilePropertiesProcessorCallback(Paths.get(appFileLocation == null ? "." : appFileLocation).toAbsolutePath().normalize()));
     } catch (CWLPortProcessorException e) {
       throw new CWLPortProcessorException("Failed to set input file properties", e);
     }
   }
-
-  public Map<String, Object> setPathsToInputs(Map<String, Object> inputs) throws CWLPortProcessorException {
-    try {
-      return portProcessor.processInputs(inputs, new CWLFileLocationToPathProcessorCallback(this.portProcessor.getJob().getApp().getAppFileLocation()));
-    } catch (CWLPortProcessorException e) {
-      throw new CWLPortProcessorException("Failed to set paths", e);
-    }
-  }
 
   public Map<String, Object> createFileLiteralFiles(Map<String, Object> inputs, Path workingDir) throws CWLPortProcessorException {
     try {

rabix-bindings-draft2/src/main/java/org/rabix/bindings/draft2/processor/callback/Draft2PortProcessorHelper.java

@@ -101,7 +101,8 @@ public Map<String, Object> stageInputFiles(Map<String, Object> inputs, File work
 
   public Map<String, Object> setFileProperties(Map<String, Object> inputs) throws Draft2PortProcessorException {
     try {
-      return portProcessor.processInputs(inputs, new Draft2FilePropertiesProcessorCallback(Paths.get(draft2Job.getApp().getAppFileLocation())));
+      String appFileLocation = draft2Job.getApp().getAppFileLocation();
+      return portProcessor.processInputs(inputs, new Draft2FilePropertiesProcessorCallback(Paths.get(appFileLocation == null ? "." : appFileLocation).toAbsolutePath().normalize()));
     } catch (Draft2PortProcessorException e) {
       throw new Draft2PortProcessorException("Failed to set input properties.", e);
     }

rabix-bindings-draft3/src/main/java/org/rabix/bindings/draft3/processor/callback/Draft3PortProcessorHelper.java

@@ -89,7 +89,8 @@ public Map<String, Object> stageInputFiles(Map<String, Object> inputs, File work
 
   public Map<String, Object> setFileProperties(Map<String, Object> inputs) throws Draft3PortProcessorException {
     try {
-      return portProcessor.processInputs(inputs, new Draft3FilePropertiesProcessorCallback(Paths.get(draft3Job.getApp().getAppFileLocation())));
+      String appFileLocation = this.draft3Job.getApp().getAppFileLocation();
+      return portProcessor.processInputs(inputs, new Draft3FilePropertiesProcessorCallback(Paths.get(appFileLocation == null ? "." : appFileLocation).toAbsolutePath().normalize()));
     } catch (Draft3PortProcessorException e) {
       throw new Draft3PortProcessorException("Failed to set input properties.", e);
     }

rabix-bindings-sb/src/main/java/org/rabix/bindings/sb/helper/SBFileValueHelper.java

@@ -71,7 +71,7 @@ public static void setChecksum(Path actual, Object raw, HashAlgorithm hashAlgori
       setValue(KEY_CHECKSUM, checksum, raw);
     }
   }
-  
+
   public static void setChecksum(String checksum, Object raw) {
     setValue(KEY_CHECKSUM, checksum, raw);
   }
@@ -92,7 +92,7 @@ public static void setContents(Object raw) throws IOException {
   public static String getContents(Object raw) {
     return getValue(KEY_CONTENTS, raw);
   }
-  
+
   private static void setContents(String contents, Map<String, Object> raw) {
     setValue(KEY_CONTENTS, contents, raw);
   }
@@ -108,19 +108,19 @@ public static String getPath(Object raw) {
   public static void setPath(String path, Object raw) {
     setValue(KEY_PATH, path, raw);
   }
-  
+
   public static String getLocation(Object raw) {
     return getValue(KEY_LOCATION, raw);
   }
 
   public static void setLocation(String location, Object raw) {
     setValue(KEY_LOCATION, location, raw);
   }
-  
+
   public static void setOriginalPath(String path, Object raw) {
     setValue(KEY_ORIGINAL_PATH, path, raw);
   }
-  
+
   public static String getOriginalPath(Object raw) {
     return getValue(KEY_ORIGINAL_PATH, raw);
   }
@@ -168,7 +168,7 @@ public static Set<String> flattenPaths(Object value) {
     }
     return paths;
   }
-  
+
   /**
    * Load first CONTENTS_NUMBER_OF_BYTES bytes from file
    */
@@ -179,7 +179,7 @@ private static String loadContents(Object fileData) throws IOException {
     try {
       File file = new File(path);
       is = new FileInputStream(file);
-      int bufferSize = file.length() > 0 && file.length() < CONTENTS_NUMBER_OF_BYTES ? (int) file.length(): CONTENTS_NUMBER_OF_BYTES;
+      int bufferSize = file.length() > 0 && file.length() < CONTENTS_NUMBER_OF_BYTES ? (int) file.length() : CONTENTS_NUMBER_OF_BYTES;
       byte[] buffer = new byte[bufferSize];
       is.read(buffer);
       return new String(buffer, "UTF-8");
@@ -193,7 +193,7 @@ private static String loadContents(Object fileData) throws IOException {
       }
     }
   }
-  
+
   public static FileValue createFileValue(Object value) {
     String path = SBFileValueHelper.getPath(value);
     String name = SBFileValueHelper.getName(value);
@@ -202,7 +202,7 @@ public static FileValue createFileValue(Object value) {
     String contents = SBFileValueHelper.getContents(value);
     String dirname = SBFileValueHelper.getDirname(value);
     Long size = SBFileValueHelper.getSize(value);
-    
+
     Map<String, Object> properties = new HashMap<>();
     properties.put(SBBindingHelper.KEY_SBG_METADATA, SBFileValueHelper.getMetadata(value));
 
@@ -218,10 +218,10 @@ public static FileValue createFileValue(Object value) {
     ret.setDirname(dirname);
     return ret;
   }
-  
+
   public static Map<String, Object> createFileRaw(FileValue fileValue) {
     Map<String, Object> raw = new HashMap<>();
-    
+
     setFileType(raw);
     setPath(fileValue.getPath(), raw);
     setName(fileValue.getName(), raw);
@@ -235,7 +235,7 @@ public static Map<String, Object> createFileRaw(FileValue fileValue) {
     if (properties != null) {
       setMetadata(properties.get(SBBindingHelper.KEY_SBG_METADATA), raw);
     }
-    
+
     List<FileValue> secondaryFileValues = fileValue.getSecondaryFiles();
     if (secondaryFileValues != null) {
       List<Map<String, Object>> secondaryFilesRaw = new ArrayList<>();
@@ -254,13 +254,7 @@ public static void buildMissingInfo(Object value, HashAlgorithm alg, Path workDi
 
     if (path == null) {
       if (location != null) {
-        URI uri = URI.create(location);
-        if (uri.getScheme() == null) {
-          uri = new URI("file", location, null);
-        }
-        if (uri.isOpaque()) {
-          uri = new URI("file", workDir.resolve(uri.getSchemeSpecificPart()).toAbsolutePath().toString(), null);
-        }
+        URI uri = createFullURI(location, workDir);
         location = uri.toString();
         actual = Paths.get(uri);
         if (!actual.isAbsolute()) {
@@ -271,17 +265,17 @@ public static void buildMissingInfo(Object value, HashAlgorithm alg, Path workDi
         return;
       }
     }
-    
+
     if (location == null) {
       actual = workDir.resolve(path).toAbsolutePath();
       location = actual.toUri().toString();
     } else {
-      actual = Paths.get(URI.create(location));
+      actual = Paths.get(createFullURI(location, workDir));
     }
-    if(!Paths.get(path).isAbsolute()){
-      path=workDir.resolve(path).toAbsolutePath().toString();
+    if (!Paths.get(path).isAbsolute()) {
+      path = workDir.resolve(path).toAbsolutePath().toString();
     }
-    
+
     String name = getName(value);
     if (name == null) {
       setNames(actual, value);
@@ -290,10 +284,10 @@ public static void buildMissingInfo(Object value, HashAlgorithm alg, Path workDi
         path = Paths.get(path).resolveSibling(name).toString();
       }
     }
-    
+
     setPath(path, value);
     setLocation(location, value);
-    
+
     if (getSize(value) == null && Files.exists(actual)) {
       setSize(Files.size(actual), value);
       if (alg != null)
@@ -311,6 +305,17 @@ public static void buildMissingInfo(Object value, HashAlgorithm alg, Path workDi
     }
   }
 
+  private static URI createFullURI(String val, Path parent) throws URISyntaxException {
+    URI uri = URI.create(val);
+    if (uri.getScheme() == null) {
+      uri = new URI("file", val, null);
+    }
+    if (uri.isOpaque()) {
+      uri = new URI("file", parent.resolve(uri.getSchemeSpecificPart()).toAbsolutePath().toString(), null);
+    }
+    return uri;
+  }
+
   private static void setNames(Path path, Object value) throws IOException {
     String name = path.getFileName().toString();
     if (getName(value) == null)

rabix-bindings-sb/src/main/java/org/rabix/bindings/sb/processor/callback/SBPortProcessorHelper.java

@@ -117,7 +117,8 @@ public Map<String, Object> setInputSecondaryFiles(Map<String, Object> inputs, SB
 
   public Map<String, Object> setFileProperties(Map<String, Object> inputs) throws SBPortProcessorException {
     try {
-      return portProcessor.processInputs(inputs, new SBFilePropertiesProcessorCallback(Paths.get(sbJob.getApp().getAppFileLocation())));
+      String appFileLocation = sbJob.getApp().getAppFileLocation();
+      return portProcessor.processInputs(inputs, new SBFilePropertiesProcessorCallback(Paths.get(appFileLocation == null ? "." : appFileLocation).toAbsolutePath().normalize()));
     } catch (SBPortProcessorException e) {
       throw new SBPortProcessorException("Failed to set inputs properties.", e);
     }

rabix-cli/src/main/java/org/rabix/cli/BackendCommandLine.java

@@ -36,6 +36,7 @@
 import org.rabix.bindings.Bindings;
 import org.rabix.bindings.BindingsFactory;
 import org.rabix.bindings.ProtocolType;
+import org.rabix.bindings.helper.FileValueHelper;
 import org.rabix.bindings.model.Application;
 import org.rabix.bindings.model.ApplicationPort;
 import org.rabix.bindings.model.DataType;
@@ -406,6 +407,20 @@ protected void configure() {
       Object commonInputs = null;
       try {       
         commonInputs = bindings.translateToCommon(inputs);
+        if (inputsFile != null) {
+          final Path finalInputs = inputsFile;
+          FileValueHelper.updateFileValues(commonInputs, (FileValue f) -> {
+            String path = f.getPath();
+            if (path != null && !Paths.get(path).isAbsolute()) {
+              f.setPath(finalInputs.resolveSibling(path).normalize().toString());
+            }
+            String location = f.getLocation();
+            if (location != null && URI.create(location).getScheme() == null) {
+              f.setLocation(finalInputs.resolveSibling(location).normalize().toString());
+            }
+            return f;
+          });
+        }
       } catch (BindingException e1) {
         VerboseLogger.log("Failed to translate inputs to the common Rabix format");
         System.exit(10);