Package: cwltool / 1.0.20181217162649+dfsg-10

add-exec-line Patch series | download
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From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Add #!/usr/bin/env cwl-runner to *.cwl
Forwarded: https://github.com/common-workflow-language/cwltool/pull/1023
--- cwltool.orig/tests/override/env-tool.cwl
+++ cwltool/tests/override/env-tool.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
--- cwltool.orig/tests/override/env-tool_v1.1.0-dev1.cwl
+++ cwltool/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:
--- cwltool.orig/tests/utf_doc_example.cwl
+++ cwltool/tests/utf_doc_example.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 inputs:
--- cwltool.orig/tests/wf/910.cwl
+++ cwltool/tests/wf/910.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 
--- cwltool.orig/tests/wf/count-lines1-wf.cwl
+++ cwltool/tests/wf/count-lines1-wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 requirements:
--- cwltool.orig/tests/wf/default-dir5.cwl
+++ cwltool/tests/wf/default-dir5.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs: []
@@ -18,4 +19,4 @@
             class: Directory
             location: inp1
       outputs: []
-      arguments: [echo, $(inputs.inp2)]
\ No newline at end of file
+      arguments: [echo, $(inputs.inp2)]
--- cwltool.orig/tests/wf/default-wf5.cwl
+++ cwltool/tests/wf/default-wf5.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 inputs: []
@@ -10,4 +11,4 @@
   step1:
     in: []
     out: []
-    run: default-dir5.cwl
\ No newline at end of file
+    run: default-dir5.cwl
--- cwltool.orig/tests/wf/expect_packed.cwl
+++ cwltool/tests/wf/expect_packed.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 {
     "$graph": [
         {
--- cwltool.orig/tests/wf/malformed_outputs.cwl
+++ cwltool/tests/wf/malformed_outputs.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
--- cwltool.orig/tests/wf/networkaccess-fail.cwl
+++ cwltool/tests/wf/networkaccess-fail.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 requirements:
@@ -12,4 +13,4 @@
   - "-c"
   - valueFrom: |
       import urllib.request
-      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
\ No newline at end of file
+      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
--- cwltool.orig/tests/wf/networkaccess.cwl
+++ cwltool/tests/wf/networkaccess.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
@@ -14,4 +15,4 @@
   - "-c"
   - valueFrom: |
       import urllib.request
-      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
\ No newline at end of file
+      assert(urllib.request.urlopen("http://commonwl.org").code == 200)
--- cwltool.orig/tests/wf/sec-tool.cwl
+++ cwltool/tests/wf/sec-tool.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
@@ -6,4 +7,4 @@
     secondaryFiles:
       - .idx
 outputs: []
-baseCommand: "true"
\ No newline at end of file
+baseCommand: "true"
--- cwltool.orig/tests/wf/sec-wf-out.cwl
+++ cwltool/tests/wf/sec-wf-out.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 inputs: []
--- cwltool.orig/tests/wf/sec-wf.cwl
+++ cwltool/tests/wf/sec-wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: Workflow
 cwlVersion: v1.0
 inputs:
--- cwltool.orig/tests/wf/secret_job.cwl
+++ cwltool/tests/wf/secret_job.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 $namespaces:
--- cwltool.orig/tests/wf/secret_wf.cwl
+++ cwltool/tests/wf/secret_wf.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 $namespaces:
--- cwltool.orig/tests/wf/separate_without_prefix.cwl
+++ cwltool/tests/wf/separate_without_prefix.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand: echo
--- cwltool.orig/tests/wf/timelimit-fail.cwl
+++ cwltool/tests/wf/timelimit-fail.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
--- cwltool.orig/tests/wf/timelimit.cwl
+++ cwltool/tests/wf/timelimit.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
--- cwltool.orig/tests/wf/trick_defaults.cwl
+++ cwltool/tests/wf/trick_defaults.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 inputs:
@@ -12,4 +13,4 @@
       class: Directory
       location: indir1
 outputs: []
-baseCommand: true
\ No newline at end of file
+baseCommand: true
--- cwltool.orig/tests/wf/vf-concat.cwl
+++ cwltool/tests/wf/vf-concat.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 requirements:
--- cwltool.orig/tests/wf/workreuse-fail.cwl
+++ cwltool/tests/wf/workreuse-fail.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 requirements:
@@ -14,4 +15,4 @@
   - "-c"
   - valueFrom: |
       import time
-      print(time.time())
\ No newline at end of file
+      print(time.time())
--- cwltool.orig/tests/wf/workreuse.cwl
+++ cwltool/tests/wf/workreuse.cwl
@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 class: CommandLineTool
 cwlVersion: v1.0
 $namespaces:
@@ -16,4 +17,4 @@
   - "-c"
   - valueFrom: |
       import time
-      print(time.time())
\ No newline at end of file
+      print(time.time())
--- cwltool.orig/tests/test_pack.py
+++ cwltool/tests/test_pack.py
@@ -1,10 +1,11 @@
-import json
 import os
 import tempfile
 from functools import partial
 
 from six import StringIO
 import pytest
+import json
+from ruamel import yaml
 
 import cwltool.pack
 import cwltool.workflow
@@ -25,7 +26,7 @@
         document_loader, workflowobj, uri, [], {})
 
     with open(get_data("tests/wf/expect_packed.cwl")) as packed_file:
-        expect_packed = json.load(packed_file)
+        expect_packed = yaml.load(packed_file)
 
     packed = cwltool.pack.pack(document_loader, processobj, uri, metadata)
     adjustFileObjs(packed, partial(make_relative, os.path.abspath(get_data("tests/wf"))))