Only bindmount basedirs.

Author: DailyDreaming

cwltool/command_line_tool.py

@@ -877,8 +877,13 @@ def update_status_output_callback(
             )
             _logger.debug("[job %s] %s", j.name, json_dumps(builder.job, indent=4))
 
+        separateDirs = True
+        # sufficient conditional for docker/singularity?
+        if runtimeContext.use_container:
+            separateDirs = False
+
         builder.pathmapper = self.make_path_mapper(
-            reffiles, builder.stagedir, runtimeContext, True
+            reffiles, builder.stagedir, runtimeContext, separateDirs
         )
         builder.requirements = j.requirements
 

cwltool/docker.py

@@ -251,6 +251,9 @@ def append_volume(
         runtime: List[str], source: str, target: str, writable: bool = False
     ) -> None:
         """Add binding arguments to the runtime list."""
+        if os.path.isfile(source) and target.endswith(os.path.basename(source)) and not writable:
+            source = os.path.dirname(source)
+            target = os.path.dirname(target)
         options = [
             "type=bind",
             "source=" + source,
@@ -260,8 +263,9 @@ def append_volume(
             options.append("readonly")
         output = StringIO()
         csv.writer(output).writerow(options)
-        mount_arg = output.getvalue().strip()
-        runtime.append("--mount={}".format(mount_arg))
+        mount_arg = f"--mount={output.getvalue().strip()}"
+        if mount_arg not in runtime:
+            runtime.append(mount_arg)
         # Unlike "--volume", "--mount" will fail if the volume doesn't already exist.
         if not os.path.exists(source):
             os.makedirs(source)

cwltool/job.py

@@ -681,10 +681,34 @@ def add_volumes(
         any_path_okay: bool = False,
     ) -> None:
         """Append volume mappings to the runtime option list."""
-        staging_dir = tempfile.mkdtemp()
-        pathmapper.reset_stagedir(staging_dir)
-        stage_files(pathmapper, symlink=False)
-        self.append_volume(runtime, staging_dir, staging_dir)
+        container_outdir = self.builder.outdir
+        for key, vol in (itm for itm in pathmapper.items() if itm[1].staged):
+            host_outdir_tgt = None  # type: Optional[str]
+            if vol.target.startswith(container_outdir + "/"):
+                host_outdir_tgt = os.path.join(
+                    self.outdir, vol.target[len(container_outdir) + 1 :]
+                )
+            if not host_outdir_tgt and not any_path_okay:
+                raise WorkflowException(
+                    "No mandatory DockerRequirement, yet path is outside "
+                    "the designated output directory, also know as "
+                    "$(runtime.outdir): {}".format(vol)
+                )
+            if vol.type in ("File", "Directory"):
+                self.add_file_or_directory_volume(runtime, vol, host_outdir_tgt)
+            elif vol.type == "WritableFile":
+                self.add_writable_file_volume(
+                    runtime, vol, host_outdir_tgt, tmpdir_prefix
+                )
+            elif vol.type == "WritableDirectory":
+                self.add_writable_directory_volume(
+                    runtime, vol, host_outdir_tgt, tmpdir_prefix
+                )
+            elif vol.type in ["CreateFile", "CreateWritableFile"]:
+                new_path = self.create_file_and_add_volume(
+                    runtime, vol, host_outdir_tgt, secret_store, tmpdir_prefix
+                )
+                pathmapper.update(key, new_path, vol.target, vol.type, vol.staged)
 
     def run(
         self,

cwltool/pathmapper.py

@@ -64,18 +64,10 @@ def __init__(
         separateDirs: bool = True,
     ) -> None:
         """Initialize the PathMapper."""
-        self.referenced_files = dedup(referenced_files)
-        self.basedir = basedir
         self._pathmap = {}  # type: Dict[str, MapperEnt]
         self.stagedir = stagedir
         self.separateDirs = separateDirs
-        self.setup(self.referenced_files, basedir)
-
-    def reset_stagedir(self, stagedir: str) -> None:
-        """Changes the target stagedir for mapped files."""
-        self.stagedir = stagedir
-        self._pathmap = {}  # type: Dict[str, MapperEnt]
-        self.setup(self.referenced_files, self.basedir)
+        self.setup(dedup(referenced_files), basedir)
 
     def visitlisting(
         self,

cwltool/singularity.py

@@ -280,16 +280,17 @@ def get_from_requirements(
 
     @staticmethod
     def append_volume(
-        runtime: List[str], source: str, target: str, writable: bool = False
+            runtime: List[str], source: str, target: str, writable: bool = False
     ) -> None:
-        runtime.append("--bind")
-        runtime.append(
-            "{}:{}:{}".format(
-                docker_windows_path_adjust(source),
-                docker_windows_path_adjust(target),
-                "rw" if writable else "ro",
-            )
-        )
+        src = docker_windows_path_adjust(source)
+        dst = docker_windows_path_adjust(target)
+        writable = "rw" if writable else "ro"
+        if os.path.isfile(src) and dst.endswith(os.path.basename(src)) and writable == 'ro':
+            src = os.path.dirname(src)
+            dst = os.path.dirname(dst)
+        bind_arg = f"--bind={src}:{dst}:{writable}"
+        if bind_arg not in runtime:
+            runtime.append(bind_arg)
 
     def add_file_or_directory_volume(
         self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str]
@@ -403,17 +404,14 @@ def create_runtime(
                 )
             )
         else:
-            runtime.append("--bind")
-            runtime.append(
-                "{}:{}:rw".format(
+            runtime.append("--bind={}:{}:rw".format(
                     docker_windows_path_adjust(os.path.realpath(self.outdir)),
                     self.builder.outdir,
                 )
             )
-        runtime.append("--bind")
         tmpdir = "/tmp"  # nosec
         runtime.append(
-            "{}:{}:rw".format(
+            "--bind={}:{}:rw".format(
                 docker_windows_path_adjust(os.path.realpath(self.tmpdir)), tmpdir
             )
         )