From baa4ec1cb1e5f496af55143f379ee37fc5e228ea Mon Sep 17 00:00:00 2001
From: "David M. Rogers" <predictivestatmech@gmail.com>
Date: Thu, 25 Jan 2024 11:31:20 -0500
Subject: [PATCH 1/2] Moved download into podman and added
 action.sequence_rules

---
 contaminate/__init__.py | 10 ++++++++-
 contaminate/action.py   | 50 ++++++++++++++++++++++++++++-------------
 contaminate/podman.py   |  6 +++++
 3 files changed, 49 insertions(+), 17 deletions(-)

diff --git a/contaminate/__init__.py b/contaminate/__init__.py
index 988d600..1a21e96 100644
--- a/contaminate/__init__.py
+++ b/contaminate/__init__.py
@@ -1,3 +1,11 @@
 from .container import Container
 from .container_env import ContainerEnv
-from .action import Return, Script, Shell, Upload, Download
+from .action import (
+    Action,
+    Return,
+    Script,
+    Shell,
+    Upload,
+    Download,
+    sequence_rules
+)
diff --git a/contaminate/action.py b/contaminate/action.py
index 3cf408c..51b98cf 100644
--- a/contaminate/action.py
+++ b/contaminate/action.py
@@ -7,7 +7,7 @@ from pydantic import BaseModel, Field
 
 from .container import Container
 from .container_env import ContainerEnv
-from .podman import runcmd
+import contaminate.podman as podman
 
 class AReturn(BaseModel):
     action_type : Literal["return"] = "return"
@@ -31,25 +31,31 @@ class AShell(BaseModel):
         return c.run_shell(self.script)
 
 class AUpload(BaseModel):
+    """ Note: paths in Upload and Download
+        must be strings, since docker uses ending '/'
+        to denote moving inside a directory, as opposed to
+        overwriting.
+    """
     action_type : Literal["upload"] = "upload"
-    src         : Path # local
-    dst         : Path # remote
+    src         : str # local
+    dst         : str # remote
     extract     : bool = False # use ADD instead of COPY
 
     def __call__(self, c : Container) -> Container:
-        cmd = f"COPY {self.src} {self.dst}"
+        src = podman.quote(self.src)
+        dst = podman.quote(self.dst)
+        cmd = f'COPY ["{src}", "{dst}"]'
         if self.extract:
-            cmd = f"ADD {self.src} {self.dst}"
+            cmd = f'ADD ["{src}", "{dst}"]'
         return c.run_cmd(cmd)
 
 class ADownload(BaseModel):
     action_type : Literal["download"] = "download"
-    src         : Path # remote
-    dst         : Path # local
+    src         : str # remote
+    dst         : str # local
 
     def __call__(self, c : Container) -> Container:
-        runcmd("podman", "cp",
-               f"{c.name}:{self.src}", self.dst)
+        podman.download(c.name, self.src, self.dst)
         return c
 
 ActionT = Annotated[
@@ -90,11 +96,23 @@ def Script(script : str) -> Action:
 def Shell(script : str) -> Action:
     return Action(AShell(script = script))
 
-def Upload(src : Union[str,Path], dst : Union[str,Path],
+def Upload(src : str, dst : str,
            extract : bool = False) -> Action:
-    return Action(AUpload(src=Path(src),
-                          dst=Path(dst), extract=extract))
-
-def Download(src : Union[str,Path], dst : Union[str,Path]
-             ) -> Action:
-    return Action(ADownload(src=Path(src), dst=Path(dst)))
+    return Action(AUpload(src=src,
+                          dst=dst, extract=extract))
+
+def Download(src : str, dst : str) -> Action:
+    return Action(ADownload(src=src, dst=dst))
+
+# Run a sequence of rules, saving a json state ea. time.
+def sequence_rules(rules : dict[str, Action], *steps : str) -> Container:
+    C = None
+    for s in steps:
+        result = Path(s + ".json")
+        if result.exists():
+            C = Container.load(result)
+        else:
+            assert C is not None, f"Starting file '{result}' not present."
+            C = C.run( rules[s], name = s )
+            C.store(result)
+    return C
diff --git a/contaminate/podman.py b/contaminate/podman.py
index b737887..3151190 100644
--- a/contaminate/podman.py
+++ b/contaminate/podman.py
@@ -5,6 +5,9 @@ import os
 import string
 from pathlib import Path
 
+def quote(s) -> str:
+    return str(s).replace("\\", "\\\\").replace('"', '\"')
+
 def to_oneliner(cmds):
     # process end-of-lines
     shell = ""
@@ -79,3 +82,6 @@ def build(name : str,
         if fname != "":
             os.remove(fname)
     return "\n".join(ans)
+
+def download(name, src, dst):
+    runcmd("podman", "cp", f"{c.name}:{self.src}", self.dst)
-- 
GitLab


From 4b868c566b7585d3820200c36206cf1ea4bbef1a Mon Sep 17 00:00:00 2001
From: "David M. Rogers" <predictivestatmech@gmail.com>
Date: Thu, 25 Jan 2024 11:38:27 -0500
Subject: [PATCH 2/2] Fixed potential None return.

---
 contaminate/action.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/contaminate/action.py b/contaminate/action.py
index 51b98cf..41a80c4 100644
--- a/contaminate/action.py
+++ b/contaminate/action.py
@@ -115,4 +115,5 @@ def sequence_rules(rules : dict[str, Action], *steps : str) -> Container:
             assert C is not None, f"Starting file '{result}' not present."
             C = C.run( rules[s], name = s )
             C.store(result)
+    assert C is not None, "Empty rule set."
     return C
-- 
GitLab