Working CWL files

Refs #4

Dockerfile

@@ -4,8 +4,6 @@
 # Using `./gradlew docker` to build image
 FROM openjdk:jre-alpine
 MAINTAINER Stefan Verhoeven <[email protected]>
-COPY bin /app/bin
-COPY lib /app/lib
-WORKDIR /app
-ENTRYPOINT ["/app/bin/xenon"]
-CMD ["--help"]
+COPY bin /usr/bin
+COPY lib /usr/lib
+CMD ["/usr/bin/xenon", "--help"]

README.md

@@ -18,6 +18,12 @@ xenon --adaptor ssh --json list --location localhost /etc
 xenon --adaptor ssh --json upload --source /etc/passwd --location localhost --path /tmp/copy-of-passwd 
 ```
 
+To keep password or passphrase invisible in process list put the password in a text file (eg. 'password.txt') and then use '@password.txt' as argument.
+For example:
+```
+xenon --username $USER --password @password.txt sftp --location localhost list $PWD/src
+```
+
 # Build
 
 ```

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

@@ -43,7 +43,7 @@ protected void copy(Files files, CopyInput source, CopyInput target, Boolean rec
             if (!target.path.startsWith("/") && !target.path.equals("-")) {
                 // 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));
+                targetPath = files.newPath(targetFS, workingDirectory.resolve(target.path));
             }
         }
 

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

@@ -23,7 +23,7 @@ public Subparser buildArgumentParser(Subparsers subparsers) {
                 .description("Download source file to local file");
         subparser.addArgument("source").help("Local source path").required(true);
         subparser.addArgument("target")
-            .type(Arguments.fileType().acceptSystemIn().verifyCanWriteParent())
+            .type(Arguments.fileType().acceptSystemIn())
             .help("Target path, use '-' for stdout")
             .required(true);
         subparser.addArgument("--recursive").help("Copy directories recursively").action(Arguments.storeTrue());

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

@@ -32,7 +32,7 @@ public static void main(String[] args) throws Exception {
         Main main = new Main();
         ArgumentParser parser = main.buildArgumentParser();
         Namespace res = parser.parseArgsOrFail(args);
-        LOGGER.warn(res.toString());
+        LOGGER.debug(res.toString());
         ICommand subcommand = res.get("command");
         Xenon xenon = XenonFactory.newXenon(buildXenonProperties(res));
         subcommand.run(res, xenon);

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

@@ -1,12 +1,12 @@
 package nl.esciencecenter.xenon.cli;
 
 public class UploadOutput {
-    public CwlFile source;
+    public String source;
     public String location;
     public String path;
 
     public UploadOutput(CopyInput source, CopyInput target) {
-        this.source = new CwlFile(source.path);
+        this.source = source.path;
         location = target.location;
         path = target.path;
     }

xenon-download.cwl

@@ -1,40 +1,81 @@
 #!/usr/bin/env cwl-runner
+# Native:
+# xenon --format cwljson sftp --location localhost download $PWD/README.md copy-of-README.md
+# Using cwl-runnner:
+# ./xenon-download.cwl --certfile ~/.ssh/id_rsa --scheme sftp --location [email protected] --source $PWD/README.md --target copy-of-README.md
 cwlVersion: v1.0
 class: CommandLineTool
 doc: Download file from remote storage
-requirements:
+hints:
 - class: DockerRequirement
   # xenon-cli Docker container needs to be manually build before
   dockerImageId: nlesc/xenon-cli
+baseCommand: xenon
 arguments:
-- --json
-- download
+- prefix: --format
+  valueFrom: cwljson
+  position: 0
+- valueFrom: download
+  position: 3
 inputs:
-  scheme:
-    type: string
-    inputBinding:
-      prefix: --scheme
-      position: -1
   certfile:
     type: File?
+    doc: Certificate file
     inputBinding:
       prefix: --certfile
-      position: -1
-  location:
+      position: 0
+  username:
     type: string?
     inputBinding:
-      position: 1
-  path:
+      prefix: --username
+      position: 0
+  password:
+    type: string?
+    doc: Password, watch out do not use on systems with untrusted users
+    inputBinding:
+      prefix: --password
+      position: 0
+  scheme:
     type: string
+    doc: Scheme, eg. file, sftp, ftp
     inputBinding:
+      position: 1
+  location:
+    type: string?
+    doc: List contents of path at location
+    inputBinding:
+      prefix: --location
       position: 2
+# TODO prop should be optional, atm is must be set
+#  prop:
+#    doc: Xenon adaptor properties
+#    type:
+#      type: array
+#      items: string
+#      inputBinding:
+#        prefix: --prop
+#    inputBinding:
+#      position: 2
+  overwrite:
+    type: boolean
+    inputBinding:
+      prefix: --overwrite
+      position: 4
+  ignore:
+    type: boolean
+    inputBinding:
+      prefix: --ignore
+      position: 4
+  source:
+    type: string
+    inputBinding:
+      position: 5
   target:
     type: string
     inputBinding:
-      position: 3
+      position: 6
 outputs:
   target:
     type: File
     outputBinding:
       glob: $(inputs.target)
-# stdout: cwl.output.json

xenon-ls.cwl

@@ -1,33 +1,72 @@
 #!/usr/bin/env cwl-runner
+# Native:
+# xenon --format cwljson sftp --location localhost list $PWD/
+# Using cwl-runnner:
+# ./xenon-ls.cwl --scheme sftp --location [email protected] --path $PWD --certfile ~/.ssh/id_rsa
 cwlVersion: v1.0
 class: CommandLineTool
 doc: List objects on remote storage
-requirements:
+hints:
 - class: DockerRequirement
   # xenon-cli Docker container needs to be manually build before
   dockerImageId: nlesc/xenon-cli
+baseCommand: xenon
 arguments:
-- --json
-- list
+- prefix: --format
+  valueFrom: cwljson
+  position: 0
+- valueFrom: list
+  position: 3
 inputs:
-  scheme:
-    type: string
-    inputBinding:
-      prefix: --scheme
-      position: -1
   certfile:
     type: File?
+    doc: Certificate file
     inputBinding:
       prefix: --certfile
-      position: -1
-  location:
+      position: 0
+  username:
     type: string?
+    inputBinding:
+      prefix: --username
+      position: 0
+  password:
+    type: string?
+    doc: Password, watch out do not use on systems with untrusted users
+    inputBinding:
+      prefix: --password
+      position: 0
+  scheme:
+    type: string
+    doc: Scheme, eg. file, sftp, ftp
     inputBinding:
       position: 1
+  location:
+    type: string?
+    doc: List contents of path at location
+    inputBinding:
+      prefix: --location
+      position: 2
+# TODO prop should be optional, atm is must be set
+#  prop:
+#    doc: Xenon adaptor properties
+#    type:
+#      type: array
+#      items: string
+#      inputBinding:
+#        prefix: --prop
+#    inputBinding:
+#      position: 2
+  recursive:
+    doc: List directories recursively
+    type: boolean?
+    inputBinding:
+      prefix: --recursive
+      position: 4
   path:
     type: string
+    doc: List contents of path at location
     inputBinding:
-      position: 2
+      position: 5
 outputs:
   objects:
     type:

xenon-upload.cwl

@@ -1,37 +1,78 @@
 #!/usr/bin/env cwl-runner
+# Native:
+# xenon --format cwljson sftp --location localhost upload README.md $PWD/copy-of-README.md
+# Using cwl-runnner:
+# ./xenon-upload.cwl --certfile ~/.ssh/id_rsa --scheme sftp --location [email protected] --source README.md --target $PWD/copy-of-README.md
 cwlVersion: v1.0
 class: CommandLineTool
 doc: Upload file to remote storage
-requirements:
+hints:
 - class: DockerRequirement
   # xenon-cli Docker container needs to be manually build before
   dockerImageId: nlesc/xenon-cli
+baseCommand: xenon
 arguments:
-- --json
-- upload
+- prefix: --format
+  valueFrom: cwljson
+  position: 0
+- valueFrom: upload
+  position: 3
 inputs:
-  scheme:
-    type: string
-    inputBinding:
-      prefix: --scheme
-      position: -1
   certfile:
     type: File?
+    doc: Certificate file
     inputBinding:
       prefix: --certfile
-      position: -1
-  source:
-    type: File
+      position: 0
+  username:
+    type: string?
+    inputBinding:
+      prefix: --username
+      position: 0
+  password:
+    type: string?
+    doc: Password, watch out do not use on systems with untrusted users
+    inputBinding:
+      prefix: --password
+      position: 0
+  scheme:
+    type: string
+    doc: Scheme, eg. file, sftp, ftp
     inputBinding:
       position: 1
   location:
     type: string?
+    doc: List contents of path at location
     inputBinding:
+      prefix: --location
       position: 2
-  path:
+# TODO prop should be optional, atm is must be set
+#  prop:
+#    doc: Xenon adaptor properties
+#    type:
+#      type: array
+#      items: string
+#      inputBinding:
+#        prefix: --prop
+#    inputBinding:
+#      position: 2
+  overwrite:
+    type: boolean
+    inputBinding:
+      prefix: --overwrite
+      position: 4
+  ignore:
+    type: boolean
+    inputBinding:
+      prefix: --ignore
+      position: 4
+  source:
+    type: File
+    inputBinding:
+      position: 5
+  target:
     type: string
     inputBinding:
-      position: 3
-outputs:
-  path: File
+      position: 6
+outputs: []
 stdout: cwl.output.json