✅ Add test for resource inventory error message

CPAC/_entrypoints/run.py

@@ -795,7 +795,7 @@ def run_main():
                 args.data_config_file, args.participant_label, args.aws_input_creds
             )
         sub_list = sub_list_filter_by_labels(
-            sub_list, {"T1w": args.T1w_label, "bold": args.bold_label}
+            list(sub_list), {"T1w": args.T1w_label, "bold": args.bold_label}
         )
 
         # C-PAC only handles single anatomical images (for now)

CPAC/conftest.py

@@ -27,7 +27,7 @@
 def bids_examples(tmp_path_factory: TempPathFactory) -> Path:
     """Get the BIDS examples dataset."""
     example_dir = tmp_path_factory.mktemp("bids-examples")
-    if not example_dir.exists():
+    if not example_dir.exists() or not any(example_dir.iterdir()):
         Repo.clone_from(
             "https://github.com/bids-standard/bids-examples.git", str(example_dir)
         )

CPAC/pipeline/resource_inventory.py

@@ -339,7 +339,7 @@ def where_to_find(resources: list[str] | str) -> str:
     inventory = resource_inventory("CPAC")
     output = ""
     for resource in resources:
-        output += f"'{resource}' is output from:\n"
+        output += f"'{resource}' can be output from:\n"
         if resource in inventory:
             for source in inventory[resource].output_from:
                 output += f"  {source}\n"

CPAC/pipeline/test/test_engine.py

@@ -1,5 +1,27 @@
+# Copyright (C) 2021-2025  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+"""Unit tests for the C-PAC pipeline engine."""
+
+from argparse import Namespace
 import os
+from pathlib import Path
+from typing import cast
 
+from _pytest.logging import LogCaptureFixture
 import pytest
 
 from CPAC.pipeline.cpac_pipeline import (
@@ -138,17 +160,129 @@ def test_build_workflow(pipe_config, bids_dir, test_dir):
     wf.run()
 
 
+def test_missing_resource(
+    bids_examples: Path, caplog: LogCaptureFixture, tmp_path: Path
+) -> None:
+    """Test the error message thrown when a resource is missing."""
+    from datetime import datetime
+
+    import yaml
+
+    from CPAC.pipeline.cpac_runner import run
+    from CPAC.utils.bids_utils import sub_list_filter_by_labels
+    from CPAC.utils.configuration import Preconfiguration, set_subject
+    from CPAC.utils.configuration.yaml_template import create_yaml_from_template
+
+    st = datetime.now().strftime("%Y-%m-%dT%H-%M-%SZ")
+    namespace = Namespace(
+        bids_dir=str(bids_examples / "ds113b"),
+        output_dir=str(tmp_path / "output"),
+        analysis_level="test_config",
+        participant_label="sub-01",
+    )
+    c = Preconfiguration("anat-only")
+    c["pipeline_setup", "output_directory", "path"] = namespace.output_dir
+    c["pipeline_setup", "log_directory", "path"] = str(tmp_path / "logs")
+    c["pipeline_setup", "working_directory", "path"] = str(tmp_path / "work")
+    c["pipeline_setup", "system_config", "maximum_memory_per_participant"] = 1.0
+    c["pipeline_setup", "system_config", "max_cores_per_participant"] = 1
+    c["pipeline_setup", "system_config", "num_participants_at_once"] = 1
+    c["pipeline_setup", "system_config", "num_ants_threads"] = 1
+    c["pipeline_setup", "working_directory", "remove_working_dir"] = True
+    sub_list = create_cpac_data_config(
+        namespace.bids_dir,
+        namespace.participant_label,
+        None,
+        True,
+        only_one_anat=False,
+    )
+    sub_list = sub_list_filter_by_labels(list(sub_list), {"T1w": None, "bold": None})
+    for i, sub in enumerate(sub_list):
+        if isinstance(sub.get("anat"), dict):
+            for anat_key in sub["anat"]:
+                if isinstance(sub["anat"][anat_key], list) and len(
+                    sub["anat"][anat_key]
+                ):
+                    sub_list[i]["anat"][anat_key] = sub["anat"][anat_key][0]
+        if isinstance(sub.get("anat"), list) and len(sub["anat"]):
+            sub_list[i]["anat"] = sub["anat"][0]
+    data_config_file = f"cpac_data_config_{st}.yml"
+    sublogdirs = [set_subject(sub, c)[2] for sub in sub_list]
+    # write out the data configuration file
+    data_config_file = os.path.join(sublogdirs[0], data_config_file)
+    with open(data_config_file, "w", encoding="utf-8") as _f:
+        noalias_dumper = yaml.dumper.SafeDumper
+        noalias_dumper.ignore_aliases = lambda self, data: True
+        yaml.dump(sub_list, _f, default_flow_style=False, Dumper=noalias_dumper)
+
+    # update and write out pipeline config file
+    pipeline_config_file = os.path.join(sublogdirs[0], f"cpac_pipeline_config_{st}.yml")
+    with open(pipeline_config_file, "w", encoding="utf-8") as _f:
+        _f.write(create_yaml_from_template(c))
+    minimized_config = f"{pipeline_config_file[:-4]}_min.yml"
+    with open(minimized_config, "w", encoding="utf-8") as _f:
+        _f.write(create_yaml_from_template(c, import_from="blank"))
+    for config_file in (data_config_file, pipeline_config_file, minimized_config):
+        os.chmod(config_file, 0o444)  # Make config files readonly
+
+    if len(sublogdirs) > 1:
+        # If more than one run is included in the given data config
+        # file, an identical copy of the data and pipeline config
+        # will be included in the log directory for each run
+        for sublogdir in sublogdirs[1:]:
+            for config_file in (
+                data_config_file,
+                pipeline_config_file,
+                minimized_config,
+            ):
+                try:
+                    os.link(config_file, config_file.replace(sublogdirs[0], sublogdir))
+                except FileExistsError:
+                    pass
+
+    run(
+        data_config_file,
+        pipeline_config_file,
+        plugin="Linear",
+        plugin_args={
+            "n_procs": int(
+                cast(
+                    int | str,
+                    c["pipeline_setup", "system_config", "max_cores_per_participant"],
+                )
+            ),
+            "memory_gb": int(
+                cast(
+                    int | str,
+                    c[
+                        "pipeline_setup",
+                        "system_config",
+                        "maximum_memory_per_participant",
+                    ],
+                )
+            ),
+            "raise_insufficient": c[
+                "pipeline_setup", "system_config", "raise_insufficient"
+            ],
+        },
+        tracking=False,
+        test_config=namespace.analysis_level == "test_config",
+    )
+
+    assert "can be output from" in caplog.text
+
+
 # bids_dir = "/Users/steven.giavasis/data/HBN-SI_dataset/rawdata"
 # test_dir = "/test_dir"
 
 # cfg = "/Users/hecheng.jin/GitHub/DevBranch/CPAC/resources/configs/pipeline_config_monkey-ABCD.yml"
-cfg = "/Users/hecheng.jin/GitHub/pipeline_config_monkey-ABCDlocal.yml"
-bids_dir = "/Users/hecheng.jin/Monkey/monkey_data_oxford/site-ucdavis"
-test_dir = "/Users/hecheng.jin/GitHub/Test/T2preproc"
 
 # test_ingress_func_raw_data(cfg, bids_dir, test_dir)
 # test_ingress_anat_raw_data(cfg, bids_dir, test_dir)
 # test_ingress_pipeconfig_data(cfg, bids_dir, test_dir)
 # test_build_anat_preproc_stack(cfg, bids_dir, test_dir)
 if __name__ == "__main__":
+    cfg = "/Users/hecheng.jin/GitHub/pipeline_config_monkey-ABCDlocal.yml"
+    bids_dir = "/Users/hecheng.jin/Monkey/monkey_data_oxford/site-ucdavis"
+    test_dir = "/Users/hecheng.jin/GitHub/Test/T2preproc"
     test_build_workflow(cfg, bids_dir, test_dir)