Merge pull request #147 from wfcommons/test_permissions

Update permissions to get tests passing on my local machine

Author: henricasanova

tests/test_helpers.py

@@ -20,6 +20,11 @@
 
 from wfcommons.common import Workflow
 
+def _recursive_chmod(dirpath, permissions):
+            for directory, directory_name, filenames in os.walk(dirpath):
+                os.chmod(directory, permissions)
+                for filename in filenames:
+                    os.chmod(os.path.join(directory, filename), permissions)
 
 def _create_fresh_local_dir(path: str) -> pathlib.Path:
     dirpath = pathlib.Path(path)
@@ -89,6 +94,7 @@ def _start_docker_container(backend, mounted_dir, working_dir, bin_dir, command=
         volumes={mounted_dir: {'bind': mounted_dir, 'mode': 'rw'}},
         working_dir=working_dir,
         user="wfcommons",
+        privileged=True,
         tty=True,
         detach=True
     )
@@ -165,4 +171,4 @@ def _compare_workflows(workflow_1: Workflow, workflow_2: Workflow):
             # sys.stderr.write(f"WORKFLOW2 OUTPUT FILE: {output_file.file_id} {output_file.size}\n")
             workflow2_output_bytes += output_file.size
     assert (workflow1_input_bytes == workflow2_input_bytes)
-    assert (workflow1_output_bytes == workflow2_output_bytes)
+    assert (workflow1_output_bytes == workflow2_output_bytes)

tests/translators_loggers/test_translators_loggers.py

@@ -17,6 +17,7 @@
 import re
 import os
 
+from tests.test_helpers import _recursive_chmod
 from tests.test_helpers import _create_fresh_local_dir
 from tests.test_helpers import _remove_local_dir_if_it_exists
 from tests.test_helpers import _start_docker_container
@@ -304,10 +305,7 @@ def test_translator(self, backend) -> None:
 
         # Make the directory that holds the translation world-writable,
         # 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)
+        _recursive_chmod(dirpath, 0o777)
 
         # Start the Docker container
         container = _start_docker_container(backend if backend != "nextflow_subworkflow" else "nextflow", str_dirpath, str_dirpath, str_dirpath + "bin/")

tests/wfbench/test_wfbench.py

@@ -15,6 +15,7 @@
 import json
 import networkx
 
+from tests.test_helpers import _recursive_chmod
 from tests.test_helpers import _create_fresh_local_dir
 from tests.test_helpers import _start_docker_container
 from tests.test_helpers import _shutdown_docker_container_and_remove_image
@@ -158,6 +159,10 @@ def test_create_from_recipe(self) -> None:
             translator = BashTranslator(benchmark.workflow)
             translator.translate(output_folder=dirpath)
 
+            # Make the directory world-writable so that
+            # we don't have any permission shenanigans
+            _recursive_chmod(dirpath, 0o777)
+
             # Start the Docker container
             sys.stderr.write("Starting Docker container...\n")
             container = _start_docker_container("bash", str_dirpath, str_dirpath, str_dirpath + "bin/")