Run reports in a separate Python process. (#41)

The runpy module we've been using to run reports provides very little
isolation. In particular, "any side effects (such as cached imports of
other modules) will remain in place after the functions have returned".
This means that if a user splits their report into multiple files, with
one file importing another, the latter will be cached and never reloaded
by Python, even if it is modified. Similarly, if the module was already
loaded before, the report runs against old code that does not match the
files included in the packet.

Using a separate subprocess gives us a much stronger isolation,
including all global variables and not sharing any of previously loaded
modules. It means a user can run a report, modify some of the imported
code, run the report again and have this behave as expected.

The sandbox is implemented by pickling the function and its argument
into a file, starting a new Python process which unpickles the file and
calls the target. Similarly, the function's return value, or any
exception it may throw, it pickled to an output file, which is read by
the parent.

I tried to use the multiprocessing module to implement this, but it puts
inconvenient requirements on the way the top-level source file is
written. The module re-evaluates the file in the subprocess, meaning its
contents must check for `__name__ == "__main__"` to avoid doing the work
again. It also doesn't work too well with the REPL. Using our own
implementation fixes these issues.

The Packet class is refactored a little and its scope is reduced to just
creating the packet and its metadata, without inserting it into the
repository. The insertion is now handled by a separate function. This is
done as a way of distinguishing what happens in the child process and
what happens in the parent.

pyproject.toml

@@ -30,7 +30,8 @@ dependencies = [
   "jsonschema",
   "pygit2",
   "outpack-query-parser",
-  "humanize"
+  "humanize",
+  "tblib"
 ]
 
 [project.urls]
@@ -214,3 +215,7 @@ ignore_missing_imports = true
 [[tool.mypy.overrides]]
 module = "outpack_query_parser"
 ignore_missing_imports = true
+
+[[tool.mypy.overrides]]
+module = "tblib"
+ignore_missing_imports = true

src/orderly/run.py

@@ -1,14 +1,17 @@
+import runpy
 import shutil
 from pathlib import Path
 from typing import Tuple
 
 from orderly.core import Description
-from orderly.current import ActiveOrderlyContext
+from orderly.current import ActiveOrderlyContext, OrderlyCustomMetadata
 from orderly.read import orderly_read
 from outpack.ids import outpack_id
-from outpack.packet import Packet
+from outpack.metadata import MetadataCore
+from outpack.packet import Packet, insert_packet
 from outpack.root import root_open
-from outpack.util import all_normal_files, run_script
+from outpack.sandbox import run_in_sandbox
+from outpack.util import all_normal_files
 
 
 def orderly_run(
@@ -19,36 +22,89 @@ def orderly_run(
     path_src, entrypoint = _validate_src_directory(name, root)
 
     dat = orderly_read(path_src / entrypoint)
-    envir = _validate_parameters(parameters, dat["parameters"])
+    parameters = _validate_parameters(parameters, dat["parameters"])
 
     packet_id = outpack_id()
     path_dest = root.path / "draft" / name / packet_id
     path_dest.mkdir(parents=True)
 
     _copy_resources_implicit(path_src, path_dest)
 
+    metadata = run_in_sandbox(
+        _packet_builder,
+        args=(
+            root.path,
+            packet_id,
+            name,
+            path_dest,
+            path_src,
+            entrypoint,
+            parameters,
+            search_options,
+        ),
+        cwd=path_dest,
+    )
+
+    insert_packet(root, path_dest, metadata)
+
+    # This is intentionally not in a `try-finally` block. If creating the
+    # packet fails and an exception was raised, we want to keep the packet in
+    # the drafts directory for the user to examine.
+    shutil.rmtree(path_dest)
+
+    return packet_id
+
+
+def _packet_builder(
+    root, id, name, path, path_src, entrypoint, parameters, search_options
+) -> MetadataCore:
+    root = root_open(root, locate=False)
     packet = Packet(
-        root, path_dest, name, id=packet_id, locate=False, parameters=envir
+        root,
+        path,
+        name,
+        id=id,
+        locate=False,
+        parameters=parameters,
     )
+
+    packet.mark_file_immutable(entrypoint)
+
+    try:
+        orderly = _run_report_script(
+            packet, path, path_src, entrypoint, parameters, search_options
+        )
+        _check_artefacts(orderly, path)
+    except:
+        packet.end(succesful=False)
+        raise
+
+    packet.add_custom_metadata("orderly", _custom_metadata(entrypoint, orderly))
+    return packet.end()
+
+
+def _run_report_script(
+    packet, path, path_src, entrypoint, parameters, search_options
+) -> OrderlyCustomMetadata:
     try:
         with ActiveOrderlyContext(packet, path_src, search_options) as orderly:
-            packet.mark_file_immutable(entrypoint)
-            run_script(path_dest, entrypoint, envir)
+            # Calling runpy with the full path to the script gives us better
+            # tracebacks
+            runpy.run_path(
+                str(path / entrypoint),
+                init_globals=parameters,
+                run_name="__main__",
+            )
+
     except Exception as error:
-        _orderly_cleanup_failure(packet)
         # This is pretty barebones for now; we will need to do some
         # work to make sure that we retain enough contextual errors
         # for the user to see that the report failed, and that it
         # failed *because* something else failed.
         msg = "Running orderly report failed!"
         raise Exception(msg) from error
 
-    try:
-        _orderly_cleanup_success(packet, entrypoint, orderly)
-    except Exception:
-        _orderly_cleanup_failure(packet)
-        raise
-    return packet_id
+    return orderly
 
 
 def _validate_src_directory(name, root) -> Tuple[Path, str]:
@@ -105,22 +161,6 @@ def _copy_resources_implicit(src, dest):
         shutil.copy2(src / p, p_dest)
 
 
-def _orderly_cleanup_success(packet, entrypoint, orderly):
-    missing = set()
-    for artefact in orderly.artefacts:
-        for path in artefact.files:
-            if not packet.path.joinpath(path).exists():
-                missing.add(path)
-    if missing:
-        missing = ", ".join(f"'{x}'" for x in sorted(missing))
-        msg = f"Script did not produce the expected artefacts: {missing}"
-        raise Exception(msg)
-    # check files (either strict or relaxed) -- but we can't do that yet
-    packet.add_custom_metadata("orderly", _custom_metadata(entrypoint, orderly))
-    packet.end(insert=True)
-    shutil.rmtree(packet.path)
-
-
 def _custom_metadata(entrypoint, orderly):
     role = [{"path": entrypoint, "role": "orderly"}]
     for p in orderly.resources:
@@ -136,5 +176,13 @@ def _custom_metadata(entrypoint, orderly):
     }
 
 
-def _orderly_cleanup_failure(packet):
-    packet.end(insert=False)
+def _check_artefacts(metadata, path):
+    missing = set()
+    for artefact in metadata.artefacts:
+        for file in artefact.files:
+            if not path.joinpath(file).exists():
+                missing.add(file)
+    if missing:
+        missing = ", ".join(f"'{x}'" for x in sorted(missing))
+        msg = f"Script did not produce the expected artefacts: {missing}"
+        raise Exception(msg)

src/outpack/packet.py

@@ -84,7 +84,7 @@ def add_custom_metadata(self, key, value):
             raise Exception(msg)
         self.custom[key] = value
 
-    def end(self, *, insert=True):
+    def end(self, *, succesful=True):
         if self.metadata:
             msg = f"Packet '{id}' already ended"
             raise Exception(msg)
@@ -96,11 +96,14 @@ def end(self, *, insert=True):
         ]
         _check_immutable_files(self.files, self.immutable)
         self.metadata = self._build_metadata()
+
         validate(self.metadata.to_dict(), "outpack/metadata.json")
-        if insert:
-            _insert(self.root, self.path, self.metadata)
-        else:
-            _cancel(self.root, self.path, self.metadata)
+        if not succesful:
+            self.path.joinpath("outpack.json").write_text(
+                self.metadata.to_json()
+            )
+
+        return self.metadata
 
     def _build_metadata(self):
         return MetadataCore(
@@ -116,7 +119,7 @@ def _build_metadata(self):
         )
 
 
-def _insert(root, path, meta):
+def insert_packet(root, path, meta):
     # check that we have not already inserted this packet; in R we
     # look to see if it's unpacked but actually the issue is if it is
     # present as metadata at all.
@@ -141,11 +144,6 @@ def _insert(root, path, meta):
     mark_known(root, meta.id, "local", hash_meta, time.time())
 
 
-def _cancel(_root, path, meta):
-    with path.joinpath("outpack.json").open("w") as f:
-        f.write(meta.to_json())
-
-
 def _check_immutable_files(files, immutable):
     if not immutable:
         return

src/outpack/sandbox.py

@@ -0,0 +1,79 @@
+import os
+import pickle
+import subprocess
+import sys
+
+from tblib import pickling_support
+
+from outpack.util import openable_temporary_file
+
+
+def run_in_sandbox(target, args=(), cwd=None, syspath=None):
+    """
+    Run a function as a separate process.
+
+    The function, its arguments and return value must be picklable.
+
+    Parameters
+    ----------
+    target:
+        The function to run in the subprocess. This function must be accessible
+        by name from the top level of a module in order to be pickled.
+    args:
+        The arguments to be passed to the function
+    cwd:
+        The working directory in which the subprocess runs. If None, it inherits
+        the current process' working directory.
+    syspath:
+        A list of paths to be added to the child process' Python search path.
+        This is used when the target function's module is not globally
+        available.
+    """
+    with openable_temporary_file() as input_file:
+        with openable_temporary_file(mode="rb") as output_file:
+            pickle.dump((target, args), input_file)
+            input_file.flush()
+
+            cmd = [
+                sys.executable,
+                "-m",
+                "outpack.sandbox",
+                input_file.name,
+                output_file.name,
+            ]
+
+            if syspath is not None:
+                env = os.environ.copy()
+                pythonpath = ":".join(str(s) for s in syspath)
+
+                if "PYTHONPATH" in env:
+                    env["PYTHONPATH"] = f"{pythonpath}:{env['PYTHONPATH']}"
+                else:
+                    env["PYTHONPATH"] = pythonpath
+            else:
+                env = None
+
+            p = subprocess.run(cmd, cwd=cwd, env=env, check=False)  # noqa: S603
+            p.check_returncode()
+
+            (ok, value) = pickle.load(output_file)  # noqa: S301
+            if ok:
+                return value
+            else:
+                raise value
+
+
+if __name__ == "__main__":
+    with open(sys.argv[1], "rb") as input_file:
+        (target, args) = pickle.load(input_file)  # noqa: S301
+
+    try:
+        result = (True, target(*args))
+    except BaseException as e:
+        # This allows the traceback to be pickled and communicated out of the
+        # the sandbox.
+        pickling_support.install(e)
+        result = (False, e)
+
+    with open(sys.argv[2], "wb") as output_file:
+        pickle.dump(result, output_file)

src/outpack/util.py

@@ -1,6 +1,5 @@
 import datetime
 import os
-import runpy
 import tempfile
 import time
 from contextlib import contextmanager
@@ -49,15 +48,6 @@ def all_normal_files(path):
     return result
 
 
-def run_script(wd, path, init_globals):
-    with transient_working_directory(wd):
-        # other ways to do this include importlib, subprocess and
-        # multiprocess
-        runpy.run_path(
-            str(wd / path), init_globals=init_globals, run_name="__main__"
-        )
-
-
 @contextmanager
 def transient_working_directory(path):
     origin = os.getcwd()

tests/helpers/__init__.py

@@ -14,7 +14,7 @@
 from outpack.init import outpack_init
 from outpack.location import outpack_location_add_path
 from outpack.metadata import MetadataCore, PacketDepends
-from outpack.packet import Packet
+from outpack.packet import Packet, insert_packet
 from outpack.root import root_open
 from outpack.schema import outpack_schema_version
 from outpack.util import openable_temporary_file
@@ -29,15 +29,17 @@ def create_packet(root, name, *, packet_id=None, parameters=None):
     packet can be populated in the block's body. The packet gets completed and
     added to the repository when the context manager is exited.
     """
+    root = root_open(root, locate=False)
     with TemporaryDirectory() as src:
         p = Packet(root, src, name, id=packet_id, parameters=parameters)
         try:
             yield p
         except BaseException:
-            p.end(insert=False)
+            p.end(succesful=False)
             raise
         else:
-            p.end(insert=True)
+            metadata = p.end(succesful=True)
+            insert_packet(root, Path(src), metadata)
 
 
 def create_random_packet(root, name="data", *, parameters=None, packet_id=None):

tests/orderly/examples/imports/helpers.py

@@ -0,0 +1,2 @@
+def get_description():
+    return "Hello from module"

tests/orderly/examples/imports/imports.py

@@ -0,0 +1,4 @@
+import orderly
+from helpers import get_description  # type: ignore
+
+orderly.description(display=get_description())