From dc5cbb0b3cb81a698efa9c3f9027c2da288e11a1 Mon Sep 17 00:00:00 2001
From: Oleg Smirnov <osmirnov@gmail.com>
Date: Tue, 30 Jan 2024 22:01:43 +0200
Subject: [PATCH] fixes #189. Adds parent access attributes to Parameter

---
 scabha/cargo.py                 |  5 +++++
 stimela/backends/singularity.py | 29 +++++++++++++++++++++--------
 stimela/backends/utils.py       | 11 +++++++++--
 3 files changed, 35 insertions(+), 10 deletions(-)

diff --git a/scabha/cargo.py b/scabha/cargo.py
index ba85e736..37fda805 100644
--- a/scabha/cargo.py
+++ b/scabha/cargo.py
@@ -127,6 +127,11 @@ class Parameter(object):
     # if true, treat parameter as a path, and ensure that the parent directories it refers to exist
     mkdir: bool = False
 
+    # if True, and parameter is a path, access to its parent directory is required
+    access_parent_dir: bool = False
+    # if True, and parameter is a path, access to its parent directory is required in writable mode
+    write_parent_dir: bool = False
+
     # for file and dir-type parameters: if True, the file(s)/dir(s) must exist. If False, they can be missing.
     # if None, then the default logic applies: inputs must exist, and outputs don't
     must_exist: Optional[bool] = None
diff --git a/stimela/backends/singularity.py b/stimela/backends/singularity.py
index 7789d4b0..938bb334 100644
--- a/stimela/backends/singularity.py
+++ b/stimela/backends/singularity.py
@@ -106,19 +106,24 @@ def build_command_line(cab: 'stimela.kitchen.cab.Cab', backend: 'stimela.backend
                         subst: Optional[Dict[str, Any]] = None,
                         binary: Optional[str] = None,
                         simg_path: Optional[str] = None):
+    from .utils import resolve_required_mounts
+
     args = cab.flavour.get_arguments(cab, params, subst, check_executable=False)
 
     if simg_path is None:
         _, simg_path = get_image_info(cab, backend)
 
     cwd = os.getcwd()
+    bind_opts = ["--bind", f"{cwd}:{cwd}"]
+    # get extra required filesystem bindings
+    extra_bindings = resolve_required_mounts(params, cab.inputs, cab.outputs, prior_mounts={cwd: True})
+    for path in extra_bindings.keys():
+        bind_opts += ["--bind", f"{path}:{path}"]
 
-    return [binary or backend.singularity.executable or BINARY, 
-            "exec", 
-            "--containall",
-            "--bind", f"{cwd}:{cwd}",
-            "--pwd", cwd,
-            simg_path] + args
+    return  [binary or backend.singularity.executable or BINARY, 
+                "exec", 
+                "--containall", "--pwd", cwd ] + bind_opts + \
+            [simg_path] + args
 
 def build(cab: 'stimela.kitchen.cab.Cab', backend: 'stimela.backend.StimelaBackendOptions', log: logging.Logger,
           command_wrapper: Optional[Callable]=None,
@@ -254,6 +259,8 @@ def run(cab: 'stimela.kitchen.cab.Cab', params: Dict[str, Any], fqname: str,
     Returns:
         Any: return value (e.g. exit code) of content
     """
+    from .utils import resolve_required_mounts
+
     native.update_rlimits(backend.rlimits, log)
 
     # get path to image, rebuilding if backend options allow this
@@ -264,9 +271,15 @@ def run(cab: 'stimela.kitchen.cab.Cab', params: Dict[str, Any], fqname: str,
     args = [backend.singularity.executable or BINARY, 
             "exec", 
             "--containall",
-            "--bind", f"{cwd}:{cwd}",
             "--pwd", cwd,
-            simg_path] 
+            "--bind", f"{cwd}:{cwd}:rw"]
+    
+    # get extra required filesystem bindings
+    extra_bindings = resolve_required_mounts(params, cab.inputs, cab.outputs, prior_mounts={cwd: True})
+    for path, rw in extra_bindings.items():
+        args += ["--bind", f"{path}:{path}:{'rw' if rw else 'ro'}"]
+
+    args += [simg_path]
     args += cab.flavour.get_arguments(cab, params, subst, check_executable=False)
     log.debug(f"command line is {args}")
 
diff --git a/stimela/backends/utils.py b/stimela/backends/utils.py
index 90e3fc09..aaf748ca 100644
--- a/stimela/backends/utils.py
+++ b/stimela/backends/utils.py
@@ -61,9 +61,16 @@ def add_target(path, must_exist, readwrite):
             must_exist = name in inputs            
         readwrite = schema.writable or name in outputs
 
-        # for symlink targets, we need to mount the parent directory
         for path in files:
-            add_target(path, must_exist=must_exist, readwrite=readwrite)
+            path = path.rstrip("/")
+            # check parent access
+            if schema.access_parent_dir or schema.write_parent_dir:
+                add_target(os.path.dirname(path), must_exist=True, readwrite=schema.write_parent_dir)
+            # for symlink targets, we need to mount the parent directory
+            if os.path.islink(path):
+                add_target(os.path.dirname(path), must_exist=True, readwrite=readwrite)
+            else:
+                add_target(path, must_exist=must_exist, readwrite=readwrite)
 
     
     # now eliminate unnecessary targets (those that have a parent mount with the same read/write property)