Merge pull request #18998 from bernt-matthias/docker-volume-z

Allow modes `z` and `Z` for docker volumes

lib/galaxy/tool_util/deps/container_classes.py

@@ -185,6 +185,10 @@ def parse_volume_str(rawstr: str) -> Tuple[str, str, str]:
         ('A', 'B', 'rw')
         >>> Volume.parse_volume_str('A:ro')
         ('A', 'A', 'ro')
+        >>> Volume.parse_volume_str('A:z')
+        ('A', 'A', 'z')
+        >>> Volume.parse_volume_str('A:Z')
+        ('A', 'A', 'Z')
         >>> Volume.parse_volume_str('A')
         ('A', 'A', 'rw')
         >>> Volume.parse_volume_str(' ')
@@ -207,7 +211,9 @@ def parse_volume_str(rawstr: str) -> Tuple[str, str, str]:
             target = volume_parts[1]
             mode = volume_parts[2]
         elif len(volume_parts) == 2:
-            if volume_parts[1] not in ("rw", "ro", "default_ro"):
+            # not really parsing/checking mode here, just figuring out if the 2nd component is target or mode
+            mode_parts = volume_parts[1].split(",")
+            if any(mode_part not in ("rw", "ro", "default_ro", "z", "Z") for mode_part in mode_parts):
                 source = volume_parts[0]
                 target = volume_parts[1]
                 mode = "rw"
@@ -400,6 +406,18 @@ def add_var(name, value):
         return volumes_str
 
 
+def _parse_volumes(volumes_raw: str, container_type: str) -> List[DockerVolume]:
+    """
+    >>> volumes_raw = "$galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:z,$default_file_path:z"
+    >>> volumes = _parse_volumes(volumes_raw, "docker")
+    >>> [str(v) for v in volumes]
+    ['"$galaxy_root:$galaxy_root:ro"', '"$tool_directory:$tool_directory:ro"', '"$job_directory:$job_directory:ro"', '"$working_directory:$working_directory:z"', '"$default_file_path:$default_file_path:z"']
+    """
+    preprocessed_volumes_list = preprocess_volumes(volumes_raw, container_type)
+    # TODO: Remove redundant volumes...
+    return [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
+
+
 class DockerContainer(Container, HasDockerLikeVolumes):
     container_type = DOCKER_CONTAINER_TYPE
 
@@ -439,9 +457,7 @@ def containerize_command(self, command: str) -> str:
             raise Exception(f"Cannot containerize command [{working_directory}] without defined working directory.")
 
         volumes_raw = self._expand_volume_str(self.destination_info.get("docker_volumes", "$defaults"))
-        preprocessed_volumes_list = preprocess_volumes(volumes_raw, self.container_type)
-        # TODO: Remove redundant volumes...
-        volumes = [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
+        volumes = _parse_volumes(volumes_raw, self.container_type)
         volumes_from = self.destination_info.get("docker_volumes_from", docker_util.DEFAULT_VOLUMES_FROM)
 
         docker_host_props = self.docker_host_props
@@ -560,8 +576,7 @@ def containerize_command(self, command: str) -> str:
             raise Exception(f"Cannot containerize command [{working_directory}] without defined working directory.")
 
         volumes_raw = self._expand_volume_str(self.destination_info.get("singularity_volumes", "$defaults"))
-        preprocessed_volumes_list = preprocess_volumes(volumes_raw, self.container_type)
-        volumes = [DockerVolume.from_str(v) for v in preprocessed_volumes_list]
+        volumes = _parse_volumes(volumes_raw, self.container_type)
 
         run_command = singularity_util.build_singularity_run_command(
             command,

lib/galaxy/tool_util/deps/container_volumes.py

@@ -7,7 +7,7 @@
 
 
 class ContainerVolume(metaclass=ABCMeta):
-    valid_modes = frozenset({"ro", "rw"})
+    valid_modes = frozenset({"ro", "rw", "z", "Z"})
 
     def __init__(self, path: str, host_path: Optional[str] = None, mode: Optional[str] = None):
         self.path = path
@@ -50,7 +50,7 @@ def from_str(cls, as_str: str) -> "DockerVolume":
             kwds["path"] = kwds["host_path"]
         elif len(parts) == 2:
             # /host_path:mode is not (or is no longer?) valid Docker volume syntax
-            if parts[1] in DockerVolume.valid_modes:
+            if all(mode_part in DockerVolume.valid_modes for mode_part in parts[1].split(",")):
                 kwds["mode"] = parts[1]
                 kwds["path"] = kwds["host_path"]
             else: