dir with executable file

conformance_tests.yaml

@@ -3481,3 +3481,11 @@
   output:
     their_name: "Foo Bar"
   tags: [ require, command_line_tool ]
+
+- id: input_directory_with_executable_file
+  job: tests/input_dir_with_executable_file.yaml
+  tool: tests/input_dir_with_executable_file.cwl
+  doc: Executable files in input directories retain their execute permissions
+  output:
+    args: [ "1", "two", "3" ]
+  tags: [ required, command_line_tool ]

tests/args.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 import sys
 import json
 import os

tests/cat1-testcli.cwl

@@ -6,7 +6,7 @@
     "hints": [
         {
             "class": "DockerRequirement",
-            "dockerPull": "python:2-slim"
+            "dockerPull": "docker.io/python:3-slim"
         }
     ],
     "inputs": [

tests/import_schema-def_packed.cwl

@@ -80,7 +80,7 @@
             "id": "#touch.cwl",
             "hints": [
                 {
-                    "dockerPull": "debian:stretch-slim",
+                    "dockerPull": "docker.io/debian:stable-slim",
                     "class": "DockerRequirement"
                 }
             ]

tests/index.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 
 # Toy program to generate inverted index of word to line.
 # Takes input text file on stdin and prints output index on stdout.

tests/input_dir_with_executable_file.cwl

@@ -0,0 +1,21 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.2
+class: CommandLineTool
+
+hints:
+  DockerRequirement:
+    dockerPull: docker.io/python:3-slim
+
+inputs:
+  dir_with_executable_file: Directory
+
+baseCommand: []
+
+arguments:
+ - $(inputs.dir_with_executable_file.path)/args.py
+ - "1"
+ - two
+ - "3"
+
+outputs:
+  args: string[]

tests/input_dir_with_executable_file.yaml

@@ -0,0 +1,6 @@
+dir_with_executable_file:
+  class: Directory
+  basename: foo
+  listing:
+    - class: File
+      path: args.py

tests/revsort-packed.cwl

@@ -7,7 +7,7 @@
             "hints": [
                 {
                     "class": "DockerRequirement",
-                    "dockerPull": "debian:stretch-slim"
+                    "dockerPull": "docker.io/debian:stable-slim"
                 }
             ],
             "inputs": [

tests/search.py

@@ -1,10 +1,8 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 # Toy program to search inverted index and print out each line the term
 # appears.
 
-from __future__ import print_function
-
 import sys
 
 mainfile = sys.argv[1]
@@ -23,5 +21,5 @@
         for l in main:
             linenum += 1
             if linenum in n:
-                print(linenum, l.rstrip())
+                print(f"{linenum} {l.rstrip()}")
         break

tests/subdirsecondaries/index.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python3
 
 # Toy program to generate inverted index of word to line.
 # Takes input text file on stdin and prints output index on stdout.

tests/tmap-tool.cwl

@@ -6,7 +6,7 @@
     "hints": [
         {
             "class": "DockerRequirement",
-            "dockerPull": "python:2-slim"
+            "dockerPull": "docker.io/python:3-slim"
         }
     ],
     "inputs": [