cli: fix for --target (#995)

* cli: fix for --target

* New way to format url in case of $graph workflow.
  Solves #991.

Signed-off-by: Rokas Maciulaitis <[email protected]>

* tests: for --target option

* Adding tests for `--target` option.

Signed-off-by: Rokas Maciulaitis <[email protected]>

* mark tests are requiring Docker under MS Windows

Author: roksys

cwltool/main.py

@@ -13,6 +13,7 @@
 import sys
 import time
 from codecs import StreamWriter, getwriter  # pylint: disable=unused-import
+from six.moves import urllib
 from typing import (IO, Any, Callable, Dict, Iterable, List, Mapping,
                     MutableMapping, MutableSequence, Optional, TextIO, Tuple,
                     Union, cast)
@@ -702,9 +703,13 @@ def my_represent_none(self, data):  # pylint: disable=unused-argument
 
             if args.target:
                 if isinstance(tool, Workflow):
-                    extracted = get_subgraph([document_loader.fetcher.urljoin(tool.tool["id"], "#"+r)
-                                              for r in args.target],
-                                             tool)
+                    url = urllib.parse.urlparse(tool.tool["id"])
+                    if url.fragment:
+                        extracted = get_subgraph([tool.tool["id"] + "/" + r for r in args.target], tool)
+                    else:
+                        extracted = get_subgraph([document_loader.fetcher.urljoin(tool.tool["id"], "#" + r)
+                                                 for r in args.target],
+                                                 tool)
                 else:
                     _logger.error("Can only use --target on Workflows")
                     return 1

tests/test_target.py

@@ -0,0 +1,31 @@
+from cwltool.main import main
+
+from .util import get_data, windows_needs_docker
+
+
+@windows_needs_docker
+def test_target():
+    """Test --target option successful."""
+    test_file = "tests/wf/scatter-wf4.cwl"
+    exit_code = main(['--target', 'out', get_data(test_file),
+                     '--inp1', 'INP1', '--inp2', 'INP2'])
+    assert exit_code == 0
+
+
+def test_wrong_target():
+    """Test --target option when value is wrong."""
+    test_file = "tests/wf/scatter-wf4.cwl"
+    exit_code = main(['--target', 'dummy_target',
+                     get_data(test_file),
+                     '--inp1', 'INP1', '--inp2', 'INP2'])
+    assert exit_code == 1
+
+
+@windows_needs_docker    
+def test_target_packed():
+    """Test --target option with packed workflow schema."""
+    test_file = "tests/wf/scatter-wf4.json"
+    exit_code = main(['--target', 'out',
+                     get_data(test_file),
+                     '--inp1', 'INP1', '--inp2', 'INP2'])
+    assert exit_code == 0

tests/wf/scatter-wf4.json

@@ -0,0 +1,103 @@
+{
+    "cwlVersion": "v1.0",
+    "$graph": [
+        {
+            "inputs": [
+                {
+                    "inputBinding": {},
+                    "type": "string",
+                    "id": "#echo/echo_in1"
+                },
+                {
+                    "inputBinding": {},
+                    "type": "string",
+                    "id": "#echo/echo_in2"
+                }
+            ],
+            "requirements": [
+                {
+                    "ramMin": 10,
+                    "class": "ResourceRequirement"
+                }
+            ],
+            "stdout": "step1_out",
+            "outputs": [
+                {
+                    "outputBinding": {
+                        "glob": "step1_out",
+                        "loadContents": true,
+                        "outputEval": "$(self[0].contents)"
+                    },
+                    "type": "string",
+                    "id": "#echo/echo_out"
+                }
+            ],
+            "baseCommand": "echo",
+            "class": "CommandLineTool",
+            "arguments": [
+                "-n",
+                "foo"
+            ],
+            "id": "#echo"
+        },
+        {
+            "inputs": [
+                {
+                    "type": {
+                        "items": "string",
+                        "type": "array"
+                    },
+                    "id": "#main/inp1"
+                },
+                {
+                    "type": {
+                        "items": "string",
+                        "type": "array"
+                    },
+                    "id": "#main/inp2"
+                }
+            ],
+            "requirements": [
+                {
+                    "class": "ScatterFeatureRequirement"
+                }
+            ],
+            "outputs": [
+                {
+                    "type": {
+                        "items": "string",
+                        "type": "array"
+                    },
+                    "outputSource": "#main/step1/echo_out",
+                    "id": "#main/out"
+                }
+            ],
+            "class": "Workflow",
+            "steps": [
+                {
+                    "run": "#echo",
+                    "scatter": [
+                        "#main/step1/echo_in1",
+                        "#main/step1/echo_in2"
+                    ],
+                    "in": [
+                        {
+                            "source": "#main/inp1",
+                            "id": "#main/step1/echo_in1"
+                        },
+                        {
+                            "source": "#main/inp2",
+                            "id": "#main/step1/echo_in2"
+                        }
+                    ],
+                    "scatterMethod": "dotproduct",
+                    "id": "#main/step1",
+                    "out": [
+                        "#main/step1/echo_out"
+                    ]
+                }
+            ],
+            "id": "#main"
+        }
+    ]
+}