Merge branch 'master' into accept-v1.1

Author: tetron

cwltool/builder.py

@@ -313,6 +313,7 @@ def _capture_files(f):
                         else:
                             sf_required = True
 
+
                         if "$(" in sf["pattern"] or "${" in sf["pattern"]:
                             sfpath = self.do_eval(sf["pattern"], context=datum)
                         else:

cwltool/update.py

@@ -50,7 +50,7 @@ def update_secondaryFiles(t):
         if isinstance(t, MutableSequence):
             return [{"pattern": p} for p in t]
         else:
-            return t
+            return {"pattern": t}
 
     def fix_inputBinding(t):
         for i in t["inputs"]:

tests/secondary-files-string-v1.cwl

@@ -0,0 +1,19 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand:
+- touch
+- 2.fastq
+requirements:
+- class: InitialWorkDirRequirement
+  listing:
+  - $(inputs.fasta_path)
+inputs:
+  fasta_path:
+    type: File
+    secondaryFiles: ^.fastq
+outputs:
+  fasta:
+    type: File
+    secondaryFiles: ^.fastq
+    outputBinding:
+      glob: $(inputs.fasta_path.basename)

tests/test_examples.py

@@ -790,7 +790,7 @@ def test_cid_file_w_prefix(tmpdir):
 
 @needs_docker
 class TestSecondaryFiles():
-    def test_secondary_files(self):
+    def test_secondary_files_v1_1(self):
         test_file = "secondary-files.cwl"
         test_job_file = "secondary-files-job.yml"
         try:
@@ -805,6 +805,23 @@ def test_secondary_files(self):
         assert "completed success" in stderr
         assert error_code == 0
 
+    def test_secondary_files_v1_0(self):
+        test_file = "secondary-files-string-v1.cwl"
+        test_job_file = "secondary-files-job.yml"
+        try:
+            old_umask = os.umask(stat.S_IWOTH)  # test run with umask 002
+            error_code, _, stderr = get_main_output(
+                [
+                    get_data(os.path.join("tests", test_file)),
+                    get_data(os.path.join("tests", test_job_file))
+                ]
+            )
+        finally:
+            assert stat.S_IMODE(os.stat('lsout').st_mode) == 436  # 664 in octal, '-rw-rw-r--'
+            os.umask(old_umask)  # revert back to original umask
+        assert "completed success" in stderr
+        assert error_code == 0
+
 
 @needs_docker
 class TestCache():