Handle files relative to working directory + added upload and downloa…

…d cwl tool files.

README.md

@@ -44,5 +44,8 @@ Requires `nlesc/xenon-cli` Docker image to be available locally.
 
 Example to list contents of `/etc` directory via a ssh to localhost connection with cwl-runner:
 ```
-cwl-runner xenon-ls.cwl --adaptor local --location localhost --path /etc
+./xenon-ls.cwl --scheme ssh --location <user>@<host> --path $PWD --certfile ~/.ssh/id_rsa
+./xenon-upload.cwl --scheme ssh --source $PWD/README.md --location <user>@<host> --path /tmp/copy-of-README.md --certfile ~/.ssh/id_rsa
+./xenon-download.cwl --scheme ssh --location <user>@<host> --path /tmp/copy-of-README.md --target /tmp/another-copy-of-README.md --certfile ~/.ssh/id_rsa
 ```
+(Replace `<user>@<host>` with actual username and hostname)

src/main/java/nl/esciencecenter/xenon/cli/CopyCommand.java

@@ -3,13 +3,32 @@
 import nl.esciencecenter.xenon.XenonException;
 import nl.esciencecenter.xenon.files.*;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 public abstract class CopyCommand extends XenonCommand {
+    private static final Logger LOGGER = LoggerFactory.getLogger(CopyCommand.class);
+
     protected void copy(Files files, CopyInput source, CopyInput target) throws XenonException {
         FileSystem sourceFS = files.newFileSystem(source.scheme, source.location, source.credential, source.properties);
         FileSystem targetFS = files.newFileSystem(target.scheme, target.location, target.credential, target.properties);
 
         Path sourcePath = files.newPath(sourceFS, new RelativePath(source.path));
+        if ("local".equals(source.scheme) || "file".equals(source.scheme)) {
+                if (!source.path.startsWith("/")) {
+                    // Path is relative to working directory, make it absolute
+                    RelativePath workingDirectory = new RelativePath(System.getProperty("user.dir"));
+                    sourcePath = files.newPath(sourceFS, workingDirectory.resolve(source.path));
+                }
+        }
         Path targetPath = files.newPath(targetFS, new RelativePath(target.path));
+        if ("local".equals(target.scheme) || "file".equals(target.scheme)) {
+            if (!target.path.startsWith("/")) {
+                // Path is relative to working directory, make it absolute
+                RelativePath workingDirectory = new RelativePath(System.getProperty("user.dir"));
+                sourcePath = files.newPath(sourceFS, workingDirectory.resolve(target.path));
+            }
+        }
 
         files.copy(sourcePath, targetPath, CopyOption.CREATE);
 

xenon-download.cwl

@@ -0,0 +1,40 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: Download file from remote storage
+requirements:
+- class: DockerRequirement
+  # xenon-cli Docker container needs to be manually build before
+  dockerImageId: nlesc/xenon-cli
+arguments:
+- --json
+- download
+inputs:
+  scheme:
+    type: string
+    inputBinding:
+      prefix: --scheme
+      position: -1
+  certfile:
+    type: File?
+    inputBinding:
+      prefix: --certfile
+      position: -1
+  location:
+    type: string?
+    inputBinding:
+      position: 1
+  path:
+    type: string
+    inputBinding:
+      position: 2
+  target:
+    type: string
+    inputBinding:
+      position: 3
+outputs:
+  target:
+    type: File
+    outputBinding:
+      glob: $(inputs.target)
+# stdout: cwl.output.json

xenon-ls.cwl

@@ -1,9 +1,4 @@
 #!/usr/bin/env cwl-runner
-
-# Examples:
-# xenon --adaptor ssh --json list --location localhost /etc
-# xenon --adaptor local --json list /etc
-
 cwlVersion: v1.0
 class: CommandLineTool
 doc: List objects on remote storage
@@ -15,15 +10,19 @@ arguments:
 - --json
 - list
 inputs:
-  adaptor:
+  scheme:
     type: string
     inputBinding:
-      prefix: --adaptor
+      prefix: --scheme
+      position: -1
+  certfile:
+    type: File?
+    inputBinding:
+      prefix: --certfile
       position: -1
   location:
     type: string?
     inputBinding:
-      prefix: --location
       position: 1
   path:
     type: string
@@ -34,4 +33,12 @@ outputs:
     type:
       type: array
       items: string
-stdout: cwl.output.json
+  files:
+    type:
+      type: array
+      items: string
+  directories:
+    type:
+      type: array
+      items: string
+stdout: cwl.output.json

xenon-upload.cwl

@@ -0,0 +1,37 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: Upload file to remote storage
+requirements:
+- class: DockerRequirement
+  # xenon-cli Docker container needs to be manually build before
+  dockerImageId: nlesc/xenon-cli
+arguments:
+- --json
+- upload
+inputs:
+  scheme:
+    type: string
+    inputBinding:
+      prefix: --scheme
+      position: -1
+  certfile:
+    type: File?
+    inputBinding:
+      prefix: --certfile
+      position: -1
+  source:
+    type: File
+    inputBinding:
+      position: 1
+  location:
+    type: string?
+    inputBinding:
+      position: 2
+  path:
+    type: string
+    inputBinding:
+      position: 3
+outputs:
+  path: File
+stdout: cwl.output.json