Do not strip newline character for files created in InitWorkDir

Author: Anton Khodak

cwltool/builder.py

@@ -244,8 +244,8 @@ def generate_arg(self, binding):  # type: (Dict[Text,Any]) -> List[Text]
 
         return [a for a in args if a is not None]
 
-    def do_eval(self, ex, context=None, pull_image=True, recursive=False):
-        # type: (Union[Dict[Text, Text], Text], Any, bool, bool) -> Any
+    def do_eval(self, ex, context=None, pull_image=True, recursive=False, strip_whitespace=True):
+        # type: (Union[Dict[Text, Text], Text], Any, bool, bool, bool) -> Any
         if recursive:
             if isinstance(ex, dict):
                 return {k: self.do_eval(v, context, pull_image, recursive) for k, v in iteritems(ex)}
@@ -260,4 +260,5 @@ def do_eval(self, ex, context=None, pull_image=True, recursive=False):
                                   timeout=self.timeout,
                                   debug=self.debug,
                                   js_console=self.js_console,
-                                  force_docker_pull=self.force_docker_pull)
+                                  force_docker_pull=self.force_docker_pull,
+                                  strip_whitespace=strip_whitespace)

cwltool/draft2tool.py

@@ -382,7 +382,7 @@ def rm_pending_output_callback(output_callbacks, jobcachepending,
             else:
                 for t in initialWorkdir["listing"]:
                     if "entry" in t:
-                        et = {u"entry": builder.do_eval(t["entry"])}
+                        et = {u"entry": builder.do_eval(t["entry"], strip_whitespace=False)}
                         if "entryname" in t:
                             et["entryname"] = builder.do_eval(t["entryname"])
                         else:

cwltool/expression.py

@@ -173,9 +173,10 @@ def evaluator(ex, jslib, obj, fullJS=False, timeout=None, force_docker_pull=Fals
 
 def interpolate(scan, rootvars,
                 timeout=None, fullJS=None, jslib="", force_docker_pull=False,
-                debug=False, js_console=False):
-    # type: (Text, Dict[Text, Any], int, bool, Union[str, Text], bool, bool, bool) -> JSON
-    scan = scan.strip()
+                debug=False, js_console=False, strip_whitespace=True):
+    # type: (Text, Dict[Text, Any], int, bool, Union[str, Text], bool, bool, bool, bool) -> JSON
+    if strip_whitespace:
+        scan = scan.strip()
     parts = []
     w = scanner(scan)
     while w:
@@ -202,8 +203,9 @@ def interpolate(scan, rootvars,
 
 
 def do_eval(ex, jobinput, requirements, outdir, tmpdir, resources,
-            context=None, pull_image=True, timeout=None, force_docker_pull=False, debug=False, js_console=False):
-    # type: (Union[dict, AnyStr], Dict[Text, Union[Dict, List, Text]], List[Dict[Text, Any]], Text, Text, Dict[Text, Union[int, Text]], Any, bool, int, bool, bool, bool) -> Any
+            context=None, pull_image=True, timeout=None, force_docker_pull=False,
+            debug=False, js_console=False, strip_whitespace=True):
+    # type: (Union[dict, AnyStr], Dict[Text, Union[Dict, List, Text]], List[Dict[Text, Any]], Text, Text, Dict[Text, Union[int, Text]], Any, bool, int, bool, bool, bool, bool) -> Any
 
     runtime = copy.copy(resources)
     runtime["tmpdir"] = docker_windows_path_adjust(tmpdir)
@@ -231,7 +233,8 @@ def do_eval(ex, jobinput, requirements, outdir, tmpdir, resources,
                                jslib=jslib,
                                force_docker_pull=force_docker_pull,
                                debug=debug,
-                               js_console=js_console)
+                               js_console=js_console,
+                               strip_whitespace=strip_whitespace)
 
         except Exception as e:
             raise WorkflowException("Expression evaluation error:\n%s" % e)

tests/test_iwdr.py

@@ -0,0 +1,16 @@
+import unittest
+
+import cwltool
+import cwltool.factory
+from tests.util import get_data
+
+
+class TestInitialWorkDir(unittest.TestCase):
+
+    def test_newline_in_entry(self):
+        """
+        test that files in InitialWorkingDirectory are created with a newline character
+        """
+        f = cwltool.factory.Factory()
+        echo = f.make(get_data("tests/wf/iwdr-entry.cwl"))
+        self.assertEqual(echo(message="hello"), {"out": "CONFIGVAR=hello\n"})

tests/wf/iwdr-entry.cwl

@@ -0,0 +1,22 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+baseCommand: ["cat", "example.conf"]
+
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: example.conf
+        entry: |
+          CONFIGVAR=$(inputs.message)
+
+inputs:
+  message: string
+outputs:
+  out:
+    type: string
+    outputBinding:
+      glob: example.conf
+      loadContents: true
+      outputEval: $(self[0].contents)