From 1eed895fcb801b2788e241587231413eb416af2e Mon Sep 17 00:00:00 2001
From: Joshua Scarsbrook <j.scarsbrook@uq.edu.au>
Date: Fri, 2 Feb 2024 01:10:53 +0000
Subject: [PATCH] added "--add" command line option to add tar files as docker
 layers. not currently supported with singularity.

---
 neurodocker/cli/generate.py                | 16 ++++++++++
 neurodocker/reproenv/renderers.py          | 18 +++++++++++
 neurodocker/reproenv/schemas/renderer.json | 36 +++++++++++++++++++++-
 3 files changed, 69 insertions(+), 1 deletion(-)

diff --git a/neurodocker/cli/generate.py b/neurodocker/cli/generate.py
index 3e1cd6a9..c0fce1c0 100644
--- a/neurodocker/cli/generate.py
+++ b/neurodocker/cli/generate.py
@@ -218,6 +218,14 @@ def _get_common_renderer_params() -> list[click.Parameter]:
                 " The last path is always the destination path in the container."
             ),
         ),
+        OptionEatAll(
+            ["--add"],
+            multiple=True,
+            type=tuple,
+            help=(
+                "Extract a tar file as a layer in the container. Provide a source and destination path."
+            ),
+        ),
         OptionEatAll(
             ["--env"],
             multiple=True,
@@ -340,6 +348,14 @@ def _get_instruction_for_param(ctx: click.Context, param: click.Parameter, value
             raise click.ClickException("expected at least two values for --copy")
         source, destination = list(value[:-1]), value[-1]
         d = {"name": param.name, "kwds": {"source": source, "destination": destination}}
+    # add
+    elif param.name == "add":
+        if not isinstance(value, tuple):
+            raise ValueError("expected this value to be a tuple (contact developers)")
+        if len(value) < 2:
+            raise click.ClickException("expected at least two values for --add")
+        source, destination = value
+        d = {"name": param.name, "kwds": {"source": source, "destination": destination}}
     # env
     elif param.name == "env":
         value = dict(value)
diff --git a/neurodocker/reproenv/renderers.py b/neurodocker/reproenv/renderers.py
index 4217d75a..83e1591b 100644
--- a/neurodocker/reproenv/renderers.py
+++ b/neurodocker/reproenv/renderers.py
@@ -373,6 +373,13 @@ def copy(
         destination: PathType | list[PathType],
     ) -> _Renderer:
         raise NotImplementedError()
+    
+    def add(
+        self,
+        source: PathType,
+        destination: PathType,
+    ) -> _Renderer:
+        raise NotImplementedError()
 
     def env(self, **kwds: str) -> _Renderer:
         raise NotImplementedError()
@@ -484,6 +491,17 @@ def copy(
         self._parts.append(s)
         return self
 
+    @_log_instruction
+    def add(
+        self,
+        source: PathType,
+        destination: PathType,
+    ) -> DockerRenderer:
+        """Add a Dockerfile `ADD` instruction."""
+        s = f"ADD {source} {destination}"
+        self._parts.append(s)
+        return self
+
     @_log_instruction
     def env(self, **kwds: str) -> DockerRenderer:
         """Add a Dockerfile `ENV` instruction."""
diff --git a/neurodocker/reproenv/schemas/renderer.json b/neurodocker/reproenv/schemas/renderer.json
index d01880de..a9b1ba23 100644
--- a/neurodocker/reproenv/schemas/renderer.json
+++ b/neurodocker/reproenv/schemas/renderer.json
@@ -50,6 +50,9 @@
           {
             "$ref": "#/definitions/copy"
           },
+          {
+            "$ref": "#/definitions/add"
+          },
           {
             "$ref": "#/definitions/env"
           },
@@ -169,6 +172,37 @@
       "examples": [],
       "additionalProperties": false
     },
+    "add": {
+      "required": [
+        "name",
+        "kwds"
+      ],
+      "properties": {
+        "name": {
+          "enum": [
+            "add"
+          ]
+        },
+        "kwds": {
+          "type": "object",
+          "required": [
+            "source",
+            "destination"
+          ],
+          "properties": {
+            "source": {
+              "type": "string"
+            },
+            "destination": {
+              "type": "string"
+            }
+          },
+          "additionalProperties": false
+        }
+      },
+      "examples": [],
+      "additionalProperties": false
+    },
     "env": {
       "required": [
         "name",
@@ -394,4 +428,4 @@
       "additionalProperties": false
     }
   }
-}
+}
\ No newline at end of file