Merge pull request #1197 from common-workflow-language/better_env_test

attempt to debug test failure on reproducible-builds.org

Author: mr-c

tests/env.cwl

@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 inputs: []

tests/env2.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+inputs: []
+requirements:
+  ShellCommandRequirement: {}
+baseCommand: echo
+arguments:
+  - valueFrom: >
+      {\\"env_listing\\": \\"\$(env)\\"}
+    shellQuote: False
+stdout: cwl.output.json
+outputs:
+  env_listing: string

tests/secondary-files-string-v1.cwl

@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand:
@@ -16,4 +17,4 @@ outputs:
     type: File
     secondaryFiles: ^.fastq
     outputBinding:
-      glob: $(inputs.fasta_path.basename)
+      glob: $(inputs.fasta_path.basename)

tests/test_examples.py

@@ -22,7 +22,7 @@
 from cwltool.resolver import Path
 from cwltool.process import CWL_IANA
 from cwltool.sandboxjs import JavascriptException
-from .util import (get_data, get_main_output, get_windows_safe_factory,
+from .util import (get_data, get_main_output, get_windows_safe_factory, subprocess,
                    needs_docker, working_directory, needs_singularity, temp_dir, windows_needs_docker)
 
 import six
@@ -1011,13 +1011,33 @@ def test_env_filtering(factor):
     commands.extend([get_data(test_file)])
     error_code, stdout, stderr = get_main_output(commands)
 
+    process = subprocess.Popen(["sh", "-c", r"""getTrueShellExeName() {
+  local trueExe nextTarget 2>/dev/null
+  trueExe=$(ps -o comm= $$) || return 1
+  [ "${trueExe#-}" = "$trueExe" ] || trueExe=${trueExe#-}
+  [ "${trueExe#/}" != "$trueExe" ] || trueExe=$([ -n "$ZSH_VERSION" ] && which -p "$trueExe" || which "$trueExe")
+  while nextTarget=$(readlink "$trueExe"); do trueExe=$nextTarget; done
+  printf '%s\n' "$(basename "$trueExe")"
+} ; getTrueShellExeName"""], stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=None)
+    sh_name, sh_name_err = process.communicate()
+    sh_name = sh_name.decode('utf-8').strip()
+
     assert "completed success" in stderr, (error_code, stdout, stderr)
     assert error_code == 0, (error_code, stdout, stderr)
     if onWindows():
         target = 5
-    else:
+    elif sh_name == "dash":
         target = 4
-    assert json.loads(stdout)['env_count'] == target, (error_code, stdout, stderr)
+    else:  # bash adds "SHLVL" and "_" environment variables
+        target = 6
+    result = json.loads(stdout)['env_count']
+    details = ''
+    if result != target:
+        _, details, _ = get_main_output(["--quiet", get_data("tests/env2.cwl")])
+        print(sh_name)
+        print(sh_name_err)
+        print(details)
+    assert result == target, (error_code, sh_name, sh_name_err, details, stdout, stderr)
 
 @windows_needs_docker
 def test_v1_0_arg_empty_prefix_separate_false():

tests/trs/md5sum-workflow.cwl

@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: Workflow
 
@@ -14,4 +15,4 @@ steps:
     run: md5sum-tool.cwl
     in:
       input_file: input_file
-    out: [output_file]
+    out: [output_file]

tests/wf/optional-numerical-output-0.cwl

@@ -1,3 +1,4 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
 baseCommand:
@@ -13,4 +14,4 @@ outputs:
     outputBinding:
       glob: "a.txt"
       loadContents: true
-      outputEval: "${\n    return parseFloat(self[0].contents);\n}"
+      outputEval: "${\n    return parseFloat(self[0].contents);\n}"