More Docker user sanitizing/fixing

Author: henricasanova

tests/test_helpers.py

@@ -50,13 +50,12 @@ def _install_WfCommons_on_container(container):
     tar_data = _make_tarfile_of_wfcommons()
     container.put_archive(target_path, tar_data)
     # Cleanup files that came from the host
-    exit_code, output = container.exec_run("sudo chown -R wfcommons:wfcommons /tmp/WfCommons", user="wfcommons", stdout=True, stderr=True)
-    exit_code, output = container.exec_run("/bin/rm -rf /tmp/WfCommons/build/", user="wfcommons", stdout=True, stderr=True)
-    exit_code, output = container.exec_run("/bin/rm -rf /tmp/WfCommons/*.egg-info/", user="wfcommons", stdout=True, stderr=True)
+    exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/build/", user="wfcommons", stdout=True, stderr=True)
+    exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/*.egg-info/", user="wfcommons", stdout=True, stderr=True)
     # Clean up and force a rebuild of cpu-benchmark (because it may be compiled for the wrong architecture)
-    exit_code, output = container.exec_run("/bin/rm -rf /tmp/WfCommons/bin/cpu-benchmark.o", user="wfcommons", stdout=True,
+    exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/bin/cpu-benchmark.o", user="wfcommons", stdout=True,
                                            stderr=True)
-    exit_code, output = container.exec_run("/bin/rm -rf /tmp/WfCommons/bin/cpu-benchmark", user="wfcommons", stdout=True,
+    exit_code, output = container.exec_run("sudo /bin/rm -rf /tmp/WfCommons/bin/cpu-benchmark", user="wfcommons", stdout=True,
                                            stderr=True)
 
     # Install WfCommons on the container (to install wfbench and cpu-benchmark really)
@@ -114,12 +113,6 @@ def _start_docker_container(backend, mounted_dir, working_dir, bin_dir, command=
     else:
         sys.stderr.write(f"[{backend}] Not Copying wfbench and cpu-benchmark...\n")
 
-    # Change file permissions
-    exit_code, output = container.exec_run(["sh", "-c", "sudo chown -R wfcommons:wfcommons ."],
-                                           user="wfcommons",
-                                           stdout=True, stderr=True)
-
-
     container.backend = backend
     return container
 

tests/translators_loggers/test_translators_loggers.py

@@ -274,8 +274,11 @@ def test_translator(self, backend) -> None:
         translator.translate(output_folder=dirpath)
 
         # Make the directory that holds the translation world-writable,
-        # so that docker commands won't fail
-        # os.chmod(dirpath, 0o777)
+        # so that we don't have any permission shenanigans
+        for directory, directory_name, filenames in os.walk(dirpath):
+            os.chmod(directory, 0o777)
+            for filename in filenames:
+                os.chmod(os.path.join(directory, filename), 0o777)
 
         # Start the Docker container
         container = _start_docker_container(backend if backend != "nextflow_subworkflow" else "nextflow", str_dirpath, str_dirpath, str_dirpath + "bin/")
@@ -289,6 +292,12 @@ def test_translator(self, backend) -> None:
         run_workflow_methods[backend](container, num_tasks, str_dirpath)
         sys.stderr.write(f"[{backend}] Workflow ran in %.2f seconds\n" % (time.time() - start_time))
 
+        # Make the whole content world-writable/readable
+        # so that we don't have any permission shenanigans for loggers below
+        exit_code, output = container.exec_run(cmd=["bash", "-c", "chmod -R 0777 ."],
+                                               user="wfcommons",
+                                               stdout=True, stderr=True)
+
         # Run the log parser if any
         if backend == "pegasus":
             parser = PegasusLogsParser(dirpath / "work/wfcommons/pegasus/Blast-Benchmark/run0001/")