Propery locate podman images

cwltool/docker.py

@@ -2,9 +2,9 @@
 
 import csv
 import datetime
+import json
 import math
 import os
-import re
 import shutil
 import subprocess  # nosec
 import sys
@@ -113,35 +113,18 @@ def get_image(
             if docker_requirement["dockerImageId"] in _IMAGES:
                 return True
 
-        for line in (
-            subprocess.check_output([self.docker_exec, "images", "--no-trunc", "--all"])  # nosec
-            .decode("utf-8")
-            .splitlines()
-        ):
+        docker_image_id = docker_requirement.get("dockerImageId")
+        if docker_image_id is not None:
             try:
-                match = re.match(r"^([^ ]+)\s+([^ ]+)\s+([^ ]+)", line)
-                split = docker_requirement["dockerImageId"].split(":")
-                if len(split) == 1:
-                    split.append("latest")
-                elif len(split) == 2:
-                    #  if split[1] doesn't  match valid tag names, it is a part of repository
-                    if not re.match(r"[\w][\w.-]{0,127}", split[1]):
-                        split[0] = split[0] + ":" + split[1]
-                        split[1] = "latest"
-                elif len(split) == 3:
-                    if re.match(r"[\w][\w.-]{0,127}", split[2]):
-                        split[0] = split[0] + ":" + split[1]
-                        split[1] = split[2]
-                        del split[2]
-
-                # check for repository:tag match or image id match
-                if match and (
-                    (split[0] == match.group(1) and split[1] == match.group(2))
-                    or docker_requirement["dockerImageId"] == match.group(3)
-                ):
-                    found = True
-                    break
-            except ValueError:
+                manifest = json.loads(
+                    subprocess.check_output(
+                        [self.docker_exec, "inspect", docker_image_id]
+                    ).decode(  # nosec
+                        "utf-8"
+                    )
+                )
+                found = manifest is not None
+            except (OSError, subprocess.CalledProcessError, UnicodeError):
                 pass
 
         if (force_pull or not found) and pull_image:

cwltool/job.py

@@ -510,17 +510,26 @@ def process_monitor(self, sproc: "subprocess.Popen[str]") -> None:
         # Value must be list rather than integer to utilise pass-by-reference in python
         memory_usage: MutableSequence[Optional[int]] = [None]
 
+        mem_tm: "Optional[Timer]" = None
+
         def get_tree_mem_usage(memory_usage: MutableSequence[Optional[int]]) -> None:
-            children = monitor.children()
             try:
-                rss = monitor.memory_info().rss
-                while len(children):
-                    rss += sum(process.memory_info().rss for process in children)
-                    children = list(itertools.chain(*(process.children() for process in children)))
-                if memory_usage[0] is None or rss > memory_usage[0]:
-                    memory_usage[0] = rss
+                with monitor.oneshot():
+                    children = monitor.children()
+                    rss = monitor.memory_info().rss
+                    while len(children):
+                        rss += sum(process.memory_info().rss for process in children)
+                        children = list(
+                            itertools.chain(*(process.children() for process in children))
+                        )
+                    if memory_usage[0] is None or rss > memory_usage[0]:
+                        memory_usage[0] = rss
+                mem_tm = Timer(interval=1, function=get_tree_mem_usage, args=(memory_usage,))
+                mem_tm.daemon = True
+                mem_tm.start()
             except psutil.NoSuchProcess:
-                mem_tm.cancel()
+                if mem_tm is not None:
+                    mem_tm.cancel()
 
         mem_tm = Timer(interval=1, function=get_tree_mem_usage, args=(memory_usage,))
         mem_tm.daemon = True
@@ -748,16 +757,6 @@ def run(
                 img_id = str(docker_req["dockerImageId"])
             elif "dockerPull" in docker_req:
                 img_id = str(docker_req["dockerPull"])
-                cmd = [user_space_docker_cmd, "pull", img_id]
-                _logger.info(str(cmd))
-                try:
-                    subprocess.check_call(cmd, stdout=sys.stderr)  # nosec
-                except OSError as exc:
-                    raise SourceLine(docker_req, None, WorkflowException, debug).makeError(
-                        f"Either Docker container {img_id} is not available with "
-                        f"user space docker implementation {user_space_docker_cmd} "
-                        f" or {user_space_docker_cmd} is missing or broken."
-                    ) from exc
             else:
                 raise SourceLine(docker_req, None, WorkflowException, debug).makeError(
                     "Docker image must be specified as 'dockerImageId' or "
@@ -1039,6 +1038,26 @@ def terminate():  # type: () -> None
             if sproc.stdin is not None:
                 sproc.stdin.close()
 
+            tm = None
+            if timelimit is not None and timelimit > 0:
+
+                def terminate():  # type: () -> None
+                    try:
+                        _logger.warning(
+                            "[job %s] exceeded time limit of %d seconds and will be terminated",
+                            name,
+                            timelimit,
+                        )
+                        sproc.terminate()
+                    except OSError:
+                        pass
+
+                tm = Timer(timelimit, terminate)
+                tm.daemon = True
+                tm.start()
+            if monitor_function:
+                monitor_function(sproc)
+
             rcode = sproc.wait()
 
             return rcode

tests/test_examples.py

@@ -1473,7 +1473,9 @@ def test_bad_userspace_runtime(factor: str) -> None:
     )
     error_code, stdout, stderr = get_main_output(commands)
     stderr = re.sub(r"\s\s+", " ", stderr)
-    assert "or quaquioN is missing or broken" in stderr, stderr
+    assert ("or quaquioN is missing or broken" in stderr) or (
+        "No such file or directory: 'quaquioN'" in stderr
+    ), stderr
     assert error_code == 1
 
 

tests/wf/timelimit.cwl

@@ -11,5 +11,5 @@ inputs:
 outputs: []
 requirements:
   cwltool:TimeLimit:
-    timelimit: 15
+    timelimit: 20
 baseCommand: sleep