Recursive pipeline submission

gaps/cli/pipeline.py

@@ -43,25 +43,60 @@ def template_pipeline_config(commands):
 
 
 @click.pass_context
-def pipeline(ctx, config_file, cancel, monitor, background=False):
+def pipeline(
+    ctx, config_file, cancel, monitor, background=False, recursive=False
+):
     """Execute multiple steps in an analysis pipeline."""
 
+    if recursive:
+        _submit_recursive_pipelines(ctx, cancel, monitor, background)
+        return
+
     if config_file is None:
-        config_file = [
-            fp
-            for fp in Path(".").glob("*")
-            if fp.is_file() and "pipeline" in fp.name
-        ]
-        if len(config_file) != 1:
+        config_files = _find_pipeline_config_files(Path("."))
+        if len(config_files) != 1:
             msg = (
                 f"Could not determine config file - multiple (or no) files "
                 f" detected with 'pipeline' in the name exist: {config_file}"
             )
             raise gapsExecutionError(msg)
 
-        config_file = config_file[0]
+        config_file = config_files[0]
 
     init_logging_from_config_file(config_file, background=background)
+    _run_pipeline(ctx, config_file, cancel, monitor, background)
+
+
+def _submit_recursive_pipelines(ctx, cancel, monitor, background):
+    """Submit pipelines in all recursive subdirectories."""
+    start_dir = Path(".")
+    for ind, sub_dir in enumerate(start_dir.glob("**/")):
+        config_files = _find_pipeline_config_files(sub_dir)
+        if sub_dir.name == Status.HIDDEN_SUB_DIR:
+            continue
+
+        if len(config_files) > 1:
+            msg = (
+                f"Could not determine config file - multiple files detected "
+                f"with 'pipeline' in the name in the {str(sub_dir)!r} "
+                "directory!"
+            )
+            warn(msg, gapsWarning)
+            continue
+        if len(config_files) == 0:
+            continue
+
+        init_logging_from_config_file(config_files[0], background=ind == 0)
+        _run_pipeline(ctx, config_files[0], cancel, monitor, background)
+
+
+def _find_pipeline_config_files(directory):
+    """Find all files matching *pipeline* in directory"""
+    return [fp for fp in Path(directory).glob("*pipeline*") if fp.is_file()]
+
+
+def _run_pipeline(ctx, config_file, cancel, monitor, background):
+    """Run a GAPs pipeline for an existing config file."""
 
     if cancel:
         Pipeline.cancel_all(config_file)
@@ -128,6 +163,17 @@ def pipeline_command(template_config):
             help="Flag to monitor pipeline jobs continuously. Default is not "
             "to monitor (kick off jobs and exit).",
         ),
+        click.Option(
+            param_decls=["--recursive", "-r"],
+            is_flag=True,
+            help="Flag to recursively submit pipelines, starting from the "
+            "current directory and checking every sub-directory therein. The "
+            "`-c` option will be *completely ignored* if you use this option. "
+            "Instead, the code will check every sub-directory for exactly one "
+            "file with the word `pipeline` in it. If found, that file is "
+            "assumed to be the pipeline config and is used to kick off the "
+            "pipeline. In any other case, the directory is skipped.",
+        ),
     ]
     if _can_run_background():
         params += [

tests/cli/test_cli_pipeline.py

@@ -5,6 +5,7 @@
 """
 import os
 import json
+import shutil
 from pathlib import Path
 
 import click
@@ -34,19 +35,6 @@
 SUCCESS_CONFIG = {"test": "success"}
 
 
-@pytest.fixture
-def runnable_pipeline(tmp_path):
-    """Add run to pipeline commands for test only."""
-    try:
-        Pipeline.COMMANDS["run"] = run
-        pipe_config_fp = tmp_path / "config_pipe.json"
-        with open(pipe_config_fp, "w") as config_file:
-            json.dump(SAMPLE_CONFIG, config_file)
-        yield
-    finally:
-        Pipeline.COMMANDS.pop("run")
-
-
 @pytest.fixture
 def pipe_config_fp(tmp_path):
     """Add a sample pipeline config to a temp directory."""
@@ -57,6 +45,16 @@ def pipe_config_fp(tmp_path):
     yield pipe_config_fp
 
 
+@pytest.fixture
+def runnable_pipeline(pipe_config_fp):
+    """Add run to pipeline commands for test only."""
+    try:
+        Pipeline.COMMANDS["run"] = run
+        yield pipe_config_fp
+    finally:
+        Pipeline.COMMANDS.pop("run")
+
+
 @click.command()
 @click.option("--config", "-c", default=".", help="Path to config file")
 def run(config):
@@ -95,7 +93,6 @@ def test_pipeline_command(
     tmp_path,
     cli_runner,
     runnable_pipeline,
-    pipe_config_fp,
     assert_message_was_logged,
 ):
     """Test the pipeline_command creation."""
@@ -108,10 +105,10 @@ def test_pipeline_command(
         assert "background" in [opt.name for opt in pipe.params]
     else:
         assert "background" not in [opt.name for opt in pipe.params]
-    cli_runner.invoke(pipe, ["-c", pipe_config_fp.as_posix()] + extra_args)
+    cli_runner.invoke(pipe, ["-c", runnable_pipeline.as_posix()] + extra_args)
 
     if not extra_args:
-        cli_runner.invoke(pipe, ["-c", pipe_config_fp.as_posix()])
+        cli_runner.invoke(pipe, ["-c", runnable_pipeline.as_posix()])
     else:
         assert Status(tmp_path).get(StatusField.MONITOR_PID) == os.getpid()
 
@@ -249,5 +246,59 @@ def test_pipeline_command_with_running_pid(
     )
 
 
+def test_pipeline_command_recursive(
+    tmp_cwd, cli_runner, runnable_pipeline, assert_message_was_logged
+):
+    """Test the pipeline command with recursive directories."""
+
+    target_config_fp = tmp_cwd / "config_run.json"
+    target_config_fp.touch()
+    runnable_pipeline.rename(runnable_pipeline.parent / "config_pipeline.json")
+
+    test_dirs = [
+        tmp_cwd,
+        tmp_cwd / "test_run_2",
+        tmp_cwd / "test_run_2" / "test_run_3",
+        tmp_cwd / "test_run_4",
+        tmp_cwd / "test_run_5",
+        tmp_cwd / "test_run_6",
+    ]
+
+    for prev_dir, next_dir in zip(test_dirs[0:-1], test_dirs[1:]):
+        shutil.copytree(prev_dir, next_dir)
+
+    for test_dir in test_dirs:
+        expected_out_fp = test_dir / "config_run.json"
+        assert expected_out_fp.exists()
+        with open(expected_out_fp, "r") as config:
+            assert not config.read()
+
+    shutil.copy(
+        test_dirs[-2] / "config_pipeline.json",
+        test_dirs[-2] / "config_pipeline2.json",
+    )
+    (test_dirs[-1] / "config_pipeline.json").unlink()
+
+    pipe = pipeline_command({})
+    cli_runner.invoke(pipe, ["-r"])
+    cli_runner.invoke(pipe, ["-r"])
+
+    for test_dir in test_dirs[:-2]:
+        assert_message_was_logged(test_dir.name, "INFO")
+        with open(test_dir / "config_run.json", "r") as config:
+            assert json.load(config) == SUCCESS_CONFIG
+
+    for test_dir in test_dirs[-2:]:
+        with open(test_dir / "config_run.json", "r") as config:
+            assert not config.read()
+
+    assert_message_was_logged("Pipeline job", "INFO")
+    assert_message_was_logged("is complete.", "INFO")
+    assert_message_was_logged(
+        "Could not determine config file - multiple files detected", "WARNING"
+    )
+    assert_message_was_logged(test_dirs[-2].name, "WARNING")
+
+
 if __name__ == "__main__":
     pytest.main(["-q", "--show-capture=all", Path(__file__), "-rapP"])