Added conditional removal of cidfile_path from runtime arguments of D… (#1007)

* Added conditional removal of cidfile_path from runtime arguments of DockerCommandLineJob
* Added test to verify udocker usage does not generate cid files

Author: mb1069

cwltool/docker.py

@@ -342,27 +342,28 @@ def create_runtime(self,
         runtime.append(u"--env=HOME=%s" % self.builder.outdir)
 
         # add parameters to docker to write a container ID file
+        if runtimeContext.user_space_docker_cmd is None:
+            if runtimeContext.cidfile_dir:
+                cidfile_dir = runtimeContext.cidfile_dir
+                if not os.path.exists(str(cidfile_dir)):
+                    _logger.error("--cidfile-dir %s error:\n%s", cidfile_dir,
+                                  "directory doesn't exist, please create it first")
+                    exit(2)
+                if not os.path.isdir(cidfile_dir):
+                    _logger.error("--cidfile-dir %s error:\n%s", cidfile_dir,
+                                  cidfile_dir + " is not a directory, "
+                                  "please check it first")
+                    exit(2)
+            else:
+                cidfile_dir = tempfile.mkdtemp(dir=runtimeContext.tmpdir_prefix)
 
-        if runtimeContext.cidfile_dir:
-            cidfile_dir = runtimeContext.cidfile_dir
-            if not os.path.exists(str(cidfile_dir)):
-                _logger.error("--cidfile-dir %s error:\n%s", cidfile_dir,
-                              "directory doesn't exist, please create it first")
-                exit(2)
-            if not os.path.isdir(cidfile_dir):
-                _logger.error("--cidfile-dir %s error:\n%s", cidfile_dir,
-                              cidfile_dir + " is not a directory, "
-                              "please check it first")
-                exit(2)
+            cidfile_name = datetime.datetime.now().strftime("%Y%m%d%H%M%S-%f") + ".cid"
+            if runtimeContext.cidfile_prefix is not None:
+                cidfile_name = str(runtimeContext.cidfile_prefix + "-" + cidfile_name)
+            cidfile_path = os.path.join(cidfile_dir, cidfile_name)
+            runtime.append(u"--cidfile=%s" % cidfile_path)
         else:
-            cidfile_dir = tempfile.mkdtemp(dir=runtimeContext.tmpdir_prefix)
-
-        cidfile_name = datetime.datetime.now().strftime("%Y%m%d%H%M%S-%f") + ".cid"
-        if runtimeContext.cidfile_prefix is not None:
-            cidfile_name = str(runtimeContext.cidfile_prefix + "-" + cidfile_name)
-        cidfile_path = os.path.join(cidfile_dir, cidfile_name)
-        runtime.append(u"--cidfile=%s" % cidfile_path)
-
+            cidfile_path = None
         for key, value in self.environment.items():
             runtime.append(u"--env=%s=%s" % (key, value))
 

tests/test_udocker.py

@@ -0,0 +1,34 @@
+import pytest
+import sys
+import os
+import subprocess
+from .util import get_data, get_main_output
+
+LINUX = sys.platform in ('linux', 'linux2')
+
+
+@pytest.mark.skipif(not LINUX, reason="LINUX only")
+def test_udocker_usage_should_not_write_cid_file(tmpdir):
+    cwd = tmpdir.chdir()
+    install_cmds = [
+        "curl https://raw.githubusercontent.com/indigo-dc/udocker/master/udocker.py -o ./udocker",
+        "chmod u+rx ./udocker",
+        "./udocker install"]
+    os.environ['UDOCKER_DIR'] = os.path.join(str(tmpdir), ".udocker")
+
+    assert sum([subprocess.call(cmd.split()) for cmd in install_cmds]) == 0
+
+    docker_path = os.path.join(str(tmpdir), 'udocker')
+
+    test_file = "tests/wf/wc-tool.cwl"
+    job_file = "tests/wf/wc-job.json"
+    error_code, stdout, stderr = get_main_output(
+        ["--debug", "--default-container", "debian", "--user-space-docker-cmd=" + docker_path,
+         get_data(test_file), get_data(job_file)])
+    cwd.chdir()
+    cidfiles_count = sum(1 for _ in tmpdir.visit(fil="*.cid"))
+
+    tmpdir.remove(ignore_errors=True)
+
+    assert "completed success" in stderr
+    assert cidfiles_count == 0