adding xarg to env command, changing output_cpath to root used in the bindings

Author: djarecka

pydra/engine/environments.py

@@ -65,46 +65,53 @@ class Container(Environment):
         Tag of the container image
     output_cpath : str
         Path to the output directory in the container
-    xargs : dict
+    xargs : Union[str, List[str]]
         Extra arguments to be passed to the container
     """
 
-    def __init__(self, image, tag="latest", output_cpath="/output_pydra", xargs=None):
+    def __init__(self, image, tag="latest", root="/mnt/pydra", xargs=None):
         self.image = image
         self.tag = tag
+        if xargs is None:
+            xargs = []
+        elif isinstance(xargs, str):
+            xargs = xargs.split()
         self.xargs = xargs
-        self.output_cpath = output_cpath
+        self.root = root
 
     @staticmethod
-    def bind(loc, mode="ro", root="/mnt/pydra"):  # TODO
-        # XXX Failure mode: {loc} overwrites a critical directory in image
-        # To fix, we'll need to update any args within loc to a new location
-        # such as /mnt/pydra/loc
+    def bind(loc, mode="ro", root="/mnt/pydra"):
         loc_abs = Path(loc).absolute()
-        return f"{loc_abs}:{root}{loc_abs}:{mode}"  # TODO: moving entire path?
+        return f"{loc_abs}:{root}{loc_abs}:{mode}"
 
 
 class Docker(Container):
     """Docker environment."""
 
-    def execute(self, task, root="/mnt/pydra"):
+    def execute(self, task):
         docker_img = f"{self.image}:{self.tag}"
         # mounting all input locations
-        mounts = task.get_bindings(root=root)
+        mounts = task.get_bindings(root=self.root)
 
         # todo adding xargsy etc
-        docker_args = ["docker", "run", "-v", self.bind(task.cache_dir, "rw")]
+        docker_args = [
+            "docker",
+            "run",
+            "-v",
+            self.bind(task.cache_dir, "rw", self.root),
+        ]
+        docker_args.extend(self.xargs)
         docker_args.extend(
             " ".join(
                 [f"-v {key}:{val[0]}:{val[1]}" for (key, val) in mounts.items()]
             ).split()
         )
-        docker_args.extend(["-w", f"{root}{task.output_dir}"])
+        docker_args.extend(["-w", f"{self.root}{task.output_dir}"])
         keys = ["return_code", "stdout", "stderr"]
         # print("\n Docker args", docker_args)
 
         values = execute(
-            docker_args + [docker_img] + task.command_args(root="/mnt/pydra"),
+            docker_args + [docker_img] + task.command_args(root=self.root),
             strip=task.strip,
         )
         output = dict(zip(keys, values))
@@ -119,28 +126,29 @@ def execute(self, task, root="/mnt/pydra"):
 class Singularity(Container):
     """Singularity environment."""
 
-    def execute(self, task, root="/mnt/pydra"):
+    def execute(self, task):
         singularity_img = f"{self.image}:{self.tag}"
         # mounting all input locations
-        mounts = task.get_bindings(root=root)
+        mounts = task.get_bindings(root=self.root)
 
         # todo adding xargsy etc
         singularity_args = [
             "singularity",
             "exec",
             "-B",
-            self.bind(task.cache_dir, "rw"),
+            self.bind(task.cache_dir, "rw", self.root),
         ]
+        singularity_args.extend(self.xargs)
         singularity_args.extend(
             " ".join(
                 [f"-B {key}:{val[0]}:{val[1]}" for (key, val) in mounts.items()]
             ).split()
         )
-        singularity_args.extend(["--pwd", f"{root}{task.output_dir}"])
+        singularity_args.extend(["--pwd", f"{self.root}{task.output_dir}"])
         keys = ["return_code", "stdout", "stderr"]
 
         values = execute(
-            singularity_args + [singularity_img] + task.command_args(root="/mnt/pydra"),
+            singularity_args + [singularity_img] + task.command_args(root=self.root),
             strip=task.strip,
         )
         output = dict(zip(keys, values))

pydra/engine/tests/test_environments.py

@@ -11,6 +11,7 @@
 from .utils import no_win, need_docker, need_singularity
 
 import attr
+import pytest
 
 
 def makedir(path, name):
@@ -79,7 +80,15 @@ def test_docker_1(tmp_path):
 
 @no_win
 @need_docker
-def test_docker_1_subm(tmp_path):
+@pytest.mark.parametrize(
+    "docker",
+    [
+        Docker(image="busybox"),
+        Docker(image="busybox", tag="latest", xargs="--rm"),
+        Docker(image="busybox", xargs=["--rm"]),
+    ],
+)
+def test_docker_1_subm(tmp_path, docker):
     """docker env with submitter: simple command, no arguments"""
     newcache = lambda x: makedir(tmp_path, x)