Merge pull request #1023 from common-workflow-language/add_exec_line

mr-c · web-flow · commit 03b817a976ed · 2019-04-22T19:32:05.000+02:00
Add #!/usr/bin/env cwl-runner to *.cwl
diff --git a/tests/override/env-tool.cwl b/tests/override/env-tool.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
diff --git a/tests/override/env-tool_v1.1.0-dev1.cwl b/tests/override/env-tool_v1.1.0-dev1.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.1.0-dev1
 inputs:
diff --git a/tests/test_pack.py b/tests/test_pack.py
@@ -1,4 +1,5 @@
 import json
+from ruamel import yaml
 import os
 import tempfile
 from functools import partial
@@ -26,7 +27,7 @@ def test_pack():
     processobj = loadingContext.loader.resolve_ref(uri)[0]
 
     with open(get_data("tests/wf/expect_packed.cwl")) as packed_file:
-        expect_packed = json.load(packed_file)
+        expect_packed = yaml.safe_load(packed_file)
 
     packed = cwltool.pack.pack(loadingContext.loader, processobj, uri, loadingContext.metadata)
     adjustFileObjs(packed, partial(make_relative, os.path.abspath(get_data("tests/wf"))))
diff --git a/tests/utf_doc_example.cwl b/tests/utf_doc_example.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:
diff --git a/tests/wf/910.cwl b/tests/wf/910.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 
diff --git a/tests/wf/count-lines1-wf.cwl b/tests/wf/count-lines1-wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 requirements:
diff --git a/tests/wf/default-dir5.cwl b/tests/wf/default-dir5.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs: []
@@ -18,4 +19,4 @@ steps:
             class: Directory
             location: inp1
       outputs: []
-      arguments: [echo, $(inputs.inp2)]
+      arguments: [echo, $(inputs.inp2)]
diff --git a/tests/wf/default-wf5.cwl b/tests/wf/default-wf5.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs: []
@@ -10,4 +11,4 @@ steps:
   step1:
     in: []
     out: []
-    run: default-dir5.cwl
+    run: default-dir5.cwl
diff --git a/tests/wf/expect_packed.cwl b/tests/wf/expect_packed.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 {
     "$graph": [
         {
diff --git a/tests/wf/malformed_outputs.cwl b/tests/wf/malformed_outputs.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/tests/wf/networkaccess-fail.cwl b/tests/wf/networkaccess-fail.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 requirements:
@@ -12,4 +13,4 @@ arguments:
   - "-c"
   - valueFrom: |
       import urllib.request
-      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
+      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
diff --git a/tests/wf/networkaccess.cwl b/tests/wf/networkaccess.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
@@ -14,4 +15,4 @@ arguments:
   - "-c"
   - valueFrom: |
       import urllib.request
-      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
+      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
diff --git a/tests/wf/sec-tool.cwl b/tests/wf/sec-tool.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
@@ -6,4 +7,4 @@ inputs:
     secondaryFiles:
       - .idx
 outputs: []
-baseCommand: "true"
+baseCommand: "true"
diff --git a/tests/wf/sec-wf-out.cwl b/tests/wf/sec-wf-out.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 inputs: []
diff --git a/tests/wf/sec-wf.cwl b/tests/wf/sec-wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 inputs:
diff --git a/tests/wf/secret_job.cwl b/tests/wf/secret_job.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 $namespaces:
diff --git a/tests/wf/secret_wf.cwl b/tests/wf/secret_wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 $namespaces:
diff --git a/tests/wf/separate_without_prefix.cwl b/tests/wf/separate_without_prefix.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
diff --git a/tests/wf/timelimit-fail.cwl b/tests/wf/timelimit-fail.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
diff --git a/tests/wf/timelimit.cwl b/tests/wf/timelimit.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
diff --git a/tests/wf/trick_defaults.cwl b/tests/wf/trick_defaults.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
@@ -12,4 +13,4 @@ inputs:
       class: Directory
       location: indir1
 outputs: []
-baseCommand: true
+baseCommand: true
diff --git a/tests/wf/vf-concat.cwl b/tests/wf/vf-concat.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 requirements:
diff --git a/tests/wf/workreuse-fail.cwl b/tests/wf/workreuse-fail.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 requirements:
@@ -14,4 +15,4 @@ arguments:
   - "-c"
   - valueFrom: |
       import time
-      print(time.time())
+      print(time.time())
diff --git a/tests/wf/workreuse.cwl b/tests/wf/workreuse.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
@@ -16,4 +17,4 @@ arguments:
   - "-c"
   - valueFrom: |
       import time
-      print(time.time())
+      print(time.time())

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+#!/usr/bin/env cwl-runner`
`1`	`2`	`class: CommandLineTool`
`2`	`3`	`cwlVersion: v1.0`
`3`	`4`	`inputs:`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+#!/usr/bin/env cwl-runner`
`1`	`2`	`class: Workflow`
`2`	`3`	`cwlVersion: v1.0`
`3`	`4`	`requirements:`
Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,4 @@`
	`1`	`+#!/usr/bin/env cwl-runner`
`1`	`2`	`{`
`2`	`3`	`"$graph": [`
`3`	`4`	`{`