Handling AvailableData entries that end up as RemoteData

src/sirocco/core/graph_items.py

@@ -51,6 +51,7 @@ def from_config(cls, config: ConfigBaseData, coordinates: dict) -> AvailableData
         data_class = AvailableData if isinstance(config, ConfigAvailableData) else GeneratedData
         return data_class(
             name=config.name,
+            computer=config.computer,
             type=config.type,
             src=config.src,
             coordinates=coordinates,

src/sirocco/workgraph.py

@@ -49,7 +49,6 @@ def _prepare_for_shell_task(task: dict, inputs: dict) -> dict:
 
     # Finally, we update the original `inputs` with the modified ones from the call to `prepare_shell_job_inputs`
     inputs = {**inputs, **aiida_shell_inputs}
-
     inputs.setdefault("metadata", {})
     inputs["metadata"].update({"call_link_label": task["name"]})
 
@@ -61,11 +60,25 @@ def _prepare_for_shell_task(task: dict, inputs: dict) -> dict:
     task_outputs = task_outputs.union(set(inputs.pop("outputs", [])))
     missing_outputs = task_outputs.difference(default_outputs)
     inputs["outputs"] = list(missing_outputs)
+
+    # NOTE: Hardcoded for now, possibly make user-facing option
+    inputs["metadata"]["options"]["use_symlinks"] = True
+
     # Workaround ends here
+    # FIXME: The `GeneratedData.name` ends up as the actual filename
+    # try:
+    #     computer = inputs['code'].computer
+    #     with computer.get_transport() as transport:
+    #         remote_is_file = transport.isfile(path=data.src)
+    # except:
+    #     raise
+
+    # import ipdb; ipdb.set_trace()
 
     return inputs
 
 
+
 aiida_workgraph.engine.utils.prepare_for_shell_task = _prepare_for_shell_task
 
 
@@ -187,13 +200,29 @@ def _add_aiida_input_data_node(self, data: core.Data):
         data_path = Path(data.src)
         data_full_path = data.src if data_path.is_absolute() else self._core_workflow.config_rootdir / data_path
 
+        # ? Explicitly check for data type "remote" ?
         if data.computer is not None:
             try:
                 computer = aiida.orm.load_computer(data.computer)
             except NotExistent as err:
                 msg = f"Could not find computer {data.computer!r} for input {data}."
                 raise ValueError(msg) from err
-            self._aiida_data_nodes[label] = aiida.orm.RemoteData(remote_path=data.src, label=label, computer=computer)
+
+            with computer.get_transport() as transport:
+                remote_is_file = transport.isfile(path=data.src)
+
+            # ? Is the `label` being used to construct the symlink
+            # TODO: If file provided as input, set the filename as label
+            # TODO: What to do for Folder
+            if not remote_is_file:
+                remote_data = aiida.orm.RemoteData(remote_path=data.src, label=label, computer=computer)
+            else:
+                # FIXME: Currently behavior of both cases is the same. Should this be handled in `aiida-shell` ???
+                # remote_data = aiida.orm.RemoteData(remote_path=str(Path(data.src).parent), label=label, computer=computer)
+                remote_data = aiida.orm.RemoteData(remote_path=data.src, label=label, computer=computer)
+
+            self._aiida_data_nodes[label] = remote_data
+
         elif data.type == "file":
             self._aiida_data_nodes[label] = aiida.orm.SinglefileData(label=label, file=data_full_path)
         elif data.type == "dir":
@@ -230,6 +259,8 @@ def _create_shell_task_node(self, task: core.ShellTask):
         # metadata
         metadata: dict[str, Any] = {}
         ## Source file
+        # FIXME: Paths are resolved to paths on the local machine if not given as absolute paths. config_rootdir points
+        # to local path, so this breaks on the remote
         env_source_paths = [
             env_source_path
             if (env_source_path := Path(env_source_file)).is_absolute()
@@ -317,6 +348,49 @@ def _set_shelljob_arguments(self, task: core.ShellTask):
         _, arguments = self.split_cmd_arg(task.resolve_ports(input_labels))
         workgraph_task_arguments.value = arguments
 
+        # filenames = []
+        # FIXME: This currently breaks...
+        # ipdb> input_socket
+        # SocketAny(name='icon_restart_date_2026_01_01_00_00_00', value=None)
+        # ipdb> workgraph_task
+        # DecoratedNode(name='icon_date_2026_03_01_00_00_00', properties=[], inputs=['metadata', 'code', 'monitors', 'remote_folder', 'nodes', 'filenames', 'arguments', 'outputs', 'parser', '_wait', 'command', 'resolve_command'], outputs=['remote_folder', 'remote_stash', 'retrieved', '_wait', '_outputs', 'stdout', 'stderr', 'icon_output', 'restart'])
+        # ipdb> workgraph_task.inputs
+        # NodeSocketNamespace(name='inputs', sockets=['metadata', 'code', 'monitors', 'remote_folder', 'nodes', 'filenames', 'arguments', 'outputs', 'parser', '_wait', 'command', 'resolve_command'])
+        # ipdb> workgraph_task.inputs.nodes
+        # TaskSocketNamespace(name='nodes', sockets=['icon_namelist', 'icon_restart_date_2026_01_01_00_00_00'])
+        # for input_socket in workgraph_task.inputs.nodes:
+        #     try:
+        #         aiida_data_node = self._aiida_data_nodes[input_socket._name]
+        #     except:
+        #         # Fails for non-existing data nodes
+        #         # Somehow restrict to only GeneratedData
+        #         continue
+        #         # import ipdb; ipdb.set_trace()
+
+        #     if isinstance(aiida_data_node, aiida.orm.FolderData):
+        #         pass
+        #     elif isinstance(aiida_data_node, aiida.orm.SinglefileData):
+        #         filenames.append(aiida_data_node.filename)
+        #         pass
+        #     elif isinstance(aiida_data_node, aiida.orm.RemoteData):
+        #         try:
+        #             # This fails if it is a file
+        #             # Could also use `.is_empty`, but seems more fragile
+        #             aiida_data_node.listdir()
+        #             remote_is_file = False
+        #         except OSError:
+        #             remote_is_file = True
+
+        #         if remote_is_file:
+        #             filenames.append(Path(aiida_data_node.get_remote_path()).name)
+        #     else:
+        #         raise Exception
+
+        # setattr(workgraph_task.inputs, "filenames", filenames)
+
+        # import ipdb; ipdb.set_trace()
+
+
     def run(
         self,
         inputs: None | dict[str, Any] = None,

tests/cases/small/config/calcinfo.json

@@ -0,0 +1,30 @@
+{
+  "codes_info": [
+    {
+      "code_uuid": "5f4a3f0d-160e-4f1d-b778-e8d584ce1b0f",
+      "cmdline_params": ["--restart", "--init", "initial_cond"],
+      "stdin_name": null,
+      "stdout_name": "stdout",
+      "stderr_name": "stderr"
+    }
+  ],
+  "append_text": "echo $? > status",
+  "remote_copy_list": [],
+  "remote_symlink_list": [
+    [
+      "da8379b9-0b77-44ad-9dc2-6b9a03d7ca2b",
+      "/mnt/home/geiger_j/test/sirocco/data/initial_conditions/*",
+      "."
+    ]
+  ],
+  "retrieve_temporary_list": [
+    "restart",
+    "icon_output",
+    "status",
+    "stderr",
+    "stdout"
+  ],
+  "provenance_exclude_list": ["input"],
+  "file_copy_operation_order": [1, 0, 2],
+  "uuid": "7683f368-c4e5-4be0-964e-28d58b88dc60"
+}

tests/cases/small/config/config-remote.yml

@@ -0,0 +1,65 @@
+---
+start_date: &root_start_date '2026-01-01T00:00'
+stop_date: &root_stop_date '2026-06-01T00:00'
+cycles:
+  - bimonthly_tasks:
+      cycling:
+        start_date: *root_start_date
+        stop_date: *root_stop_date
+        period: P2M
+      tasks:
+        - icon:
+            inputs:
+              - icon_namelist:
+                  port: UNUSED
+              - initial_cond:
+                  when:
+                    at: *root_start_date
+                  port:
+                    init
+              - icon_restart:
+                  when:
+                    after: *root_start_date
+                  target_cycle:
+                    lag: -P2M
+                  port: restart
+            outputs: [icon_output, icon_restart]
+  - lastly:
+      tasks:
+        - cleanup:
+            wait_on:
+              - icon:
+                  target_cycle:
+                    date: 2026-05-01T00:00
+tasks:
+  - icon:
+      computer: thor
+      plugin: shell
+      # src: scripts/icon.py
+      src: /mnt/home/geiger_j/test/sirocco/icon.py
+      command: "icon.py --restart {PORT::restart} --init {PORT::init}"
+      # env_source_files: data/dummy_source_file.sh
+  - cleanup:
+      computer: thor
+      plugin: shell
+      # src: scripts/cleanup.py
+      src: /mnt/home/geiger_j/test/sirocco/cleanup.py
+      command: "cleanup.py"
+data:
+  available:
+     - icon_namelist:
+         type: file
+         src: data/input
+     - initial_cond:
+         type: file
+         computer: thor
+        #  src: data/initial_conditions
+        #  src: /mnt/home/geiger_j/test/sirocco/data
+         src: /mnt/home/geiger_j/test/sirocco/data/initial_conditions
+  generated:
+     - icon_output:
+         type: file
+         src: icon_output
+     - icon_restart:
+         type: file
+         src: restart

tests/cases/small/config/config.yml

@@ -47,7 +47,8 @@ data:
   available:
      - icon_namelist:
          type: file
-         src: data/input
+        #  src: data/input
+         src: ICON/NAMELIST_exclaim_ape_R02B04
      - initial_conditions:
          type: file
          computer: localhost

tests/cases/small/config/data/dummy_source_file.sh

@@ -0,0 +1,3 @@
+#! /bin/bash
+
+: