Merge pull request #469 from simvue-io/add_process_cwd

Add cwd option to add_process

Author: kzscisoft

simvue/executor.py

@@ -40,6 +40,7 @@ def _execute_process(
     completion_callback: typing.Optional[CompletionCallback] = None,
     completion_trigger: typing.Optional[multiprocessing.synchronize.Event] = None,
     environment: typing.Optional[typing.Dict[str, str]] = None,
+    cwd: typing.Optional[pathlib.Path] = None,
 ) -> tuple[subprocess.Popen, typing.Optional[threading.Thread]]:
     thread_out = None
 
@@ -51,6 +52,7 @@ def _execute_process(
                 stderr=err,
                 universal_newlines=True,
                 env=environment,
+                cwd=cwd,
             )
 
     if completion_callback or completion_trigger:
@@ -138,6 +140,7 @@ def add_process(
         script: typing.Optional[pathlib.Path] = None,
         input_file: typing.Optional[pathlib.Path] = None,
         env: typing.Optional[typing.Dict[str, str]] = None,
+        cwd: typing.Optional[pathlib.Path] = None,
         completion_callback: typing.Optional[CompletionCallback] = None,
         completion_trigger: typing.Optional[multiprocessing.synchronize.Event] = None,
         **kwargs,
@@ -186,6 +189,8 @@ def callback_function(status_code: int, std_out: str, std_err: str) -> None:
             you should provide it as such and perform the upload manually, by default None
         env : typing.Dict[str, str], optional
             environment variables for process
+        cwd: typing.Optional[pathlib.Path], optional
+            working directory to execute the process within
         completion_callback : typing.Callable | None, optional
             callback to run when process terminates
         completion_trigger : multiprocessing.Event | None, optional
@@ -252,6 +257,7 @@ def callback_function(status_code: int, std_out: str, std_err: str) -> None:
                 completion_callback,
                 completion_trigger,
                 env,
+                cwd,
             )
         )
 

simvue/run.py

@@ -660,6 +660,7 @@ def add_process(
         ] = None,
         completion_trigger: typing.Optional[multiprocessing.synchronize.Event] = None,
         env: typing.Optional[typing.Dict[str, str]] = None,
+        cwd: typing.Optional[pathlib.Path] = None,
         **cmd_kwargs,
     ) -> None:
         """Add a process to be executed to the executor.
@@ -703,10 +704,10 @@ def callback_function(status_code: int, std_out: str, std_err: str) -> None:
             positional argument, by default None
         *positional_arguments : Any, ..., optional
             all other positional arguments are taken to be part of the command to execute
-        script : str | None, optional
+        script : pydantic.FilePath | None, optional
             the script to run, note this only work if the script is not an option, if this is the case
             you should provide it as such and perform the upload manually, by default None
-        input_file : str | None, optional
+        input_file : pydantic.FilePath | None, optional
             the input file to run, note this only work if the input file is not an option, if this is the case
             you should provide it as such and perform the upload manually, by default None
         completion_callback : typing.Callable | None, optional
@@ -715,6 +716,9 @@ def callback_function(status_code: int, std_out: str, std_err: str) -> None:
             this trigger event is set when the processes completes
         env : typing.Dict[str, str], optional
             environment variables for process
+        cwd: typing.Optional[pathlib.Path], optional
+            working directory to execute the process within. Note that executable, input and script file paths should
+            be absolute or relative to the directory where this method is called, not relative to the new working directory.
         **kwargs : Any, ..., optional
             all other keyword arguments are interpreted as options to the command
         """
@@ -773,6 +777,7 @@ def callback_function(status_code: int, std_out: str, std_err: str) -> None:
             completion_callback=completion_callback,  # type: ignore
             completion_trigger=completion_trigger,
             env=env,
+            cwd=cwd,
             **cmd_kwargs,
         )
 

tests/functional/test_run_process_cwd.py

@@ -0,0 +1,56 @@
+import unittest
+import uuid
+import tempfile
+import simvue
+from simvue import Run
+import os
+import filecmp
+import time
+class TestRunProcess(unittest.TestCase):
+    def test_processes_cwd(self):
+        """Check that cwd argument works correctly in add_process.
+
+        Create a temporary directory, and a python file inside that directory. Check that if only the file name
+        is passed to add_process as the script, and the directory is specified as the cwd argument, that the process
+        runs correctly and the script is uploaded as expected.
+        """
+        with tempfile.TemporaryDirectory() as temp_dir:
+            with tempfile.NamedTemporaryFile(dir=temp_dir, suffix=".py") as temp_file:
+                with open(temp_file.name, "w") as out_f:
+                    out_f.writelines([
+                        "import os\n",
+                        "f = open('new_file.txt', 'w')\n",
+                        "f.write('Test Line')\n",
+                        "f.close()"
+                    ])
+                    import pdb; pdb.set_trace()
+                    
+                with Run() as run:
+                    run.init(
+                        name='test-%s' % str(uuid.uuid4()),
+                        folder='/test-%s' % str(uuid.uuid4())
+                    )
+                    run_id = run._id
+                    run.add_process(
+                        identifier="sleep_10_process",
+                        executable="python",
+                        script=temp_file.name,
+                        cwd=temp_dir
+                    )
+                    time.sleep(1)
+                    run.save_file(os.path.join(temp_dir, "new_file.txt"), 'output')
+
+                client = simvue.Client()
+
+                # Check that the script was uploaded to the run correctly
+                os.makedirs(os.path.join(temp_dir, "downloaded"))
+                client.get_artifact_as_file(run_id, os.path.basename(temp_file.name), path=os.path.join(temp_dir, "downloaded"))
+                assert filecmp.cmp(os.path.join(temp_dir, "downloaded", os.path.basename(temp_file.name)), temp_file.name)
+
+                client.get_artifact_as_file(run_id, "new_file.txt", path=os.path.join(temp_dir, "downloaded"))
+                new_file = open(os.path.join(temp_dir, "downloaded", "new_file.txt"), "r")
+                assert new_file.read() == "Test Line"
+                new_file.close()
+
+if __name__ == '__main__':
+    unittest.main()