Add simple DayOA catalog smoke command

Author: iamh2o

config/daylily_available_repositories.yaml

@@ -102,6 +102,34 @@ repositories:
     default_ref: 2.0.19
     relative_path: daylily-omics-analysis
     analysis_commands:
+      - command_id: simple-test
+        display_name: "Simple Test"
+        description: "Smoke-test DayOA shell initialization and local help target without staged sample inputs."
+        datasource: DayOA
+        launcher: workflow_launch
+        command_class: utility
+        input_contract: none
+        requires_staging: false
+        requires_run_mount: false
+        runtime_parameters: {}
+        input_requirements: {}
+        targets:
+          - help
+        genome: hg38
+        jobs: 1
+        aligners: []
+        dedupers: []
+        snv_callers: []
+        sv_callers: []
+        dy_command: "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help"
+        dryrun_dy_command: "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help"
+        compatible_platforms:
+          - local
+        compatible_data_modes:
+          - none
+        git_tag: 2.0.19
+        no_containerized: true
+        validation_runs: []
       - command_id: illumina_snv_alignstats
         display_name: "Illumina SNV + Alignstats"
         description: "Illumina WGS Sentieon DNAscope and alignment-statistics launch profile."

daylily_ec/cli.py

@@ -2380,6 +2380,16 @@ def workflow_launch(
         "--stage-base",
         help="Base staging directory to scan when --stage-dir is omitted.",
     ),
+    input_staging: bool = typer.Option(
+        True,
+        "--input-staging/--no-input-staging",
+        help="Copy staged samples/units into the workflow clone.",
+    ),
+    default_activation: bool = typer.Option(
+        True,
+        "--default-activation/--no-default-activation",
+        help="Run the standard dyoainit plus Slurm day_activate setup before --dy-command.",
+    ),
     session_name: Optional[str] = typer.Option(
         None,
         "--session-name",
@@ -2566,6 +2576,10 @@ def workflow_launch(
     ):
         if value is not None:
             argv.extend([flag, value])
+    if not input_staging:
+        argv.append("--no-input-staging")
+    if not default_activation:
+        argv.append("--no-default-activation")
     argv.append("--skip-project-check" if skip_project_check else "--strict-project-check")
     if no_containerized:
         argv.append("--no-containerized")

daylily_ec/repositories.py

@@ -15,7 +15,7 @@
 
 CATALOG_VERSION = 2
 SUPPORTED_CATALOG_VERSIONS = {1, CATALOG_VERSION}
-COMMAND_CLASSES = {"sample_analysis", "run_analysis"}
+COMMAND_CLASSES = {"sample_analysis", "run_analysis", "utility"}
 INPUT_CONTRACTS = {"sample_manifest", "run_context", "none"}
 EXPORT_TRIGGERS = {"none", "on-success", "on-fail", "all"}
 VALIDATION_STATUSES = {"success", "failed", "blocked", "not_run"}
@@ -363,6 +363,13 @@ def _validate_launcher(self) -> "AnalysisCommand":
                 raise ValueError("run_analysis commands must not require sample staging")
             if not self.requires_run_mount:
                 raise ValueError("run_analysis commands must require run mounts")
+        if self.command_class == "utility":
+            if self.input_contract != "none":
+                raise ValueError("utility commands must use none input")
+            if self.requires_staging:
+                raise ValueError("utility commands must not require sample staging")
+            if self.requires_run_mount:
+                raise ValueError("utility commands must not require run mounts")
         if not self.compatible_platforms:
             raise ValueError("compatible_platforms must not be empty")
         if not self.compatible_data_modes:
@@ -500,6 +507,8 @@ def launch_argv(
         argv.append("--skip-project-check" if skip_project_check else "--strict-project-check")
         if self.no_containerized:
             argv.append("--no-containerized")
+        if self.input_contract == "none":
+            argv.extend(["--no-input-staging", "--no-default-activation"])
         if export_destination_s3_uri:
             argv.extend(["--export-destination-s3-uri", export_destination_s3_uri])
         if export_trigger != "none":

daylily_ec/resources/payload/config/daylily_available_repositories.yaml

@@ -102,6 +102,34 @@ repositories:
     default_ref: 2.0.19
     relative_path: daylily-omics-analysis
     analysis_commands:
+      - command_id: simple-test
+        display_name: "Simple Test"
+        description: "Smoke-test DayOA shell initialization and local help target without staged sample inputs."
+        datasource: DayOA
+        launcher: workflow_launch
+        command_class: utility
+        input_contract: none
+        requires_staging: false
+        requires_run_mount: false
+        runtime_parameters: {}
+        input_requirements: {}
+        targets:
+          - help
+        genome: hg38
+        jobs: 1
+        aligners: []
+        dedupers: []
+        snv_callers: []
+        sv_callers: []
+        dy_command: "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help"
+        dryrun_dy_command: "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help"
+        compatible_platforms:
+          - local
+        compatible_data_modes:
+          - none
+        git_tag: 2.0.19
+        no_containerized: true
+        validation_runs: []
       - command_id: illumina_snv_alignstats
         display_name: "Illumina SNV + Alignstats"
         description: "Illumina WGS Sentieon DNAscope and alignment-statistics launch profile."

daylily_ec/scripts/daylily_run_omics_analysis_headnode.py

@@ -214,6 +214,18 @@ def build_parser() -> argparse.ArgumentParser:
         default="/fsx/staging/staged_external_sequencing_data",
         help="Base staging directory to scan when --stage-dir is omitted",
     )
+    parser.add_argument(
+        "--no-input-staging",
+        dest="input_staging",
+        action="store_false",
+        help="Do not copy staged samples/units or write a run context before launching",
+    )
+    parser.add_argument(
+        "--no-default-activation",
+        dest="default_activation",
+        action="store_false",
+        help="Do not run the standard dyoainit plus Slurm activation before --dy-command",
+    )
     parser.add_argument(
         "--session-name",
         help="Name of the tmux session to create on the head node. Defaults to --analysis-id.",
@@ -318,7 +330,7 @@ def build_parser() -> argparse.ArgumentParser:
         help="Ursa analysis EUID linked to the exported analysis directory external object",
     )
     parser.add_argument("--dry-run", action="store_true")
-    parser.set_defaults(skip_project_check=True)
+    parser.set_defaults(skip_project_check=True, input_staging=True, default_activation=True)
     return parser
 
 
@@ -408,21 +420,27 @@ def main(argv: Optional[List[str]] = None) -> int:
 
     run_context_content: Optional[str] = None
     if args.run_context_file:
+        if not args.input_staging:
+            raise CommandError("--run-context-file cannot be used with --no-input-staging.")
         if args.stage_dir:
             raise CommandError("--stage-dir cannot be used with --run-context-file.")
         run_context_path = Path(args.run_context_file).expanduser()
         if not run_context_path.is_file():
             raise CommandError(f"Run context file not found: {run_context_path}")
         run_context_content = run_context_path.read_text(encoding="utf-8")
         stage_config = None
-    else:
+    elif args.input_staging:
         stage_config = discover_stage_config(
             target.instance_id,
             args.profile,
             region,
             args.stage_dir,
             args.stage_base,
         )
+    else:
+        if args.stage_dir:
+            raise CommandError("--stage-dir cannot be used with --no-input-staging.")
+        stage_config = None
 
     if args.dy_command:
         dy_command = args.dy_command
@@ -446,6 +464,8 @@ def main(argv: Optional[List[str]] = None) -> int:
     skip_check = "true" if args.skip_project_check else "false"
     run_context_mode = run_context_content is not None
     run_context_mode_literal = "true" if run_context_mode else "false"
+    input_staging_mode_literal = "true" if args.input_staging else "false"
+    default_activation_literal = "true" if args.default_activation else "false"
     run_context_payload = shlex.quote(run_context_content or "")
     export_destination_literal = shlex.quote(args.export_destination_s3_uri or "")
     delete_on_export_success = "true" if args.delete_on_export_success else "false"
@@ -483,6 +503,8 @@ def main(argv: Optional[List[str]] = None) -> int:
 	ANALYSIS_ID={shlex.quote(analysis_id)}
 	EXECUTING_ENTITY={shlex.quote(executing_entity)}
 	RUN_CONTEXT_MODE={run_context_mode_literal}
+	INPUT_STAGING_MODE={input_staging_mode_literal}
+	DEFAULT_ACTIVATION={default_activation_literal}
 	RUN_CONTEXT_PAYLOAD={run_context_payload}
 	STAGE_SAMPLES={shlex.quote(stage_samples_path)}
 	STAGE_UNITS={shlex.quote(stage_units_path)}
@@ -529,9 +551,11 @@ def main(argv: Optional[List[str]] = None) -> int:
 	mkdir -p config
 	if [[ "$RUN_CONTEXT_MODE" == "true" ]]; then
 	  printf '%s' "$RUN_CONTEXT_PAYLOAD" > config/runs.tsv
-	else
+	elif [[ "$INPUT_STAGING_MODE" == "true" ]]; then
 	  cp "$STAGE_SAMPLES" config/samples.tsv
 	  cp "$STAGE_UNITS" config/units.tsv
+	else
+	  echo "[INFO] Input staging skipped for this catalog command."
 	fi
 
 if [[ ! -f "$HOME/miniconda3/etc/profile.d/conda.sh" ]]; then
@@ -550,18 +574,20 @@ def main(argv: Optional[List[str]] = None) -> int:
 if [[ "$SKIP_PROJECT_CHECK" == "true" ]]; then
   dyoa_args+=(--skip-project-check)
 fi
-set +u
-. dyoainit "${{dyoa_args[@]}}"
-set -u
-set +e
-set +u
-. bin/day_activate slurm {shlex.quote(args.genome)} remote
-activate_status=$?
-set -u
-set -e
-if [[ "$activate_status" != "0" ]]; then
-  echo "[ERROR] day_activate failed with status $activate_status"
-  exit "$activate_status"
+if [[ "$DEFAULT_ACTIVATION" == "true" ]]; then
+  set +u
+  . dyoainit "${{dyoa_args[@]}}"
+  set -u
+  set +e
+  set +u
+  . bin/day_activate slurm {shlex.quote(args.genome)} remote
+  activate_status=$?
+  set -u
+  set -e
+  if [[ "$activate_status" != "0" ]]; then
+    echo "[ERROR] day_activate failed with status $activate_status"
+    exit "$activate_status"
+  fi
 fi
 set +e
 eval "$DY_COMMAND"

docs/plans/20260529T022223Z_dayoa_to_dyec_release_train_ledger.md

@@ -0,0 +1,28 @@
+# DayOA To DYEC Release Train Ledger
+
+## Objective
+Close the remaining boot-script publication gap, release the current DayOA work, release the current DYEC utility-command work, update DYEC DayOA pins to the new DayOA release, and publish a final DYEC release tag.
+
+## Gate 0 Inventory
+- DYEC repo: `/Users/jmajor/.codex/worktrees/dyec-fsx-dra-mounts/daylily-ephemeral-cluster`
+- DYEC branch: `codex/dyec-dewey-registration-refactor-20260528`
+- DYEC initial state: clean relative to origin except current uncommitted `simple-test` catalog/launcher changes.
+- DYEC latest fetched non-v semver tag before this train: `5.0.29`
+- Planned DYEC utility release tag: `5.0.30`
+- Planned DYEC pin-update release tag: `5.0.31`
+- DayOA repo: `/Users/jmajor/projects/daylily/daylily-omics-analysis`
+- DayOA branch: `codex/dayoa-local-evidence-dewey-refactor-20260528`
+- DayOA latest fetched non-v semver tag before this train: `2.0.20`
+- Intermediate DayOA release tags created in this train: `2.0.21`, `2.0.22`
+- Final DayOA pin target release tag: `2.0.23`
+- Remaining prior blocker: public Daylily boot-script object backup/upload failed with `AccessDenied` using profile `lsmc`.
+
+## Ledger
+| ID | Lane | Task | Status | Evidence | Blocker | Notes |
+| --- | --- | --- | --- | --- | --- | --- |
+| G0-001 | Inventory | Record repo state, tag baselines, and remaining publication blocker. | SUCCESS | Gate 0 inventory above. |  | This ledger coordinates DayOA and DYEC release order. |
+| PUB-001 | S3 publish | Back up and update the remaining public Daylily boot-script target, then verify readback SHA. | SUCCESS | `AWS_PROFILE=daylily` copied the current object to `s3://daylily-dayoa-references-usw2/runtime_assets/cluster_boot_config/backups/post_install_ubuntu_combined.sh.pre-overlay-removal-20260529T022223Z`, uploaded the local script, and read back SHA `4b4363ec4e123872c76498c2a5d42b91ce8c43ab376147ddd20865f0911e6a3a`, matching local. |  | No S3 deletion was performed. |
+| DAYOA-001 | DayOA release | Validate, commit, annotated-tag the DayOA release, verify, push branch and tag. | SUCCESS | DayOA focused validation passed. Tags `2.0.21`, `2.0.22`, and final pin target `2.0.23` were created as annotated tags and pushed. Final tag `2.0.23` peels to commit `3d5e86c38f1a03a2a47cbad570d4ace5386bbec6`. |  | Earlier pushed tags are preserved; DYEC pins `2.0.23`. |
+| DYEC-001 | DYEC utility release | Validate, commit current `simple-test` catalog/launcher changes, annotated-tag `5.0.30`, verify, push branch and tag. | PENDING |  |  | Keeps current dirty work as its own release. |
+| DYEC-002 | DYEC pin update | Update DYEC DayOA pins to `2.0.21`, validate, commit, annotated-tag `5.0.31`, verify, push branch and tag. | PENDING |  |  | Final DYEC tag should point to the new DayOA release. |
+| FINAL-001 | Final report | Report all release tags, pushed refs, validation, and any remaining blockers. | PENDING |  |  | Report exact tag objects and peeled commits. |

tests/test_cli_registry_v2.py

@@ -1811,6 +1811,48 @@ def fake_launch(argv: list[str]) -> int:
     assert "--stage-dir" not in argv
 
 
+def test_workflow_launch_forwards_no_input_utility_flags(monkeypatch) -> None:
+    import daylily_ec.scripts.daylily_run_omics_analysis_headnode as launch_module
+
+    calls: dict[str, object] = {}
+    _activate_dayec_runtime(monkeypatch)
+
+    def fake_launch(argv: list[str]) -> int:
+        calls["argv"] = argv
+        return 0
+
+    monkeypatch.setattr(launch_module, "main", fake_launch)
+
+    result = runner.invoke(
+        app,
+        [
+            "workflow",
+            "launch",
+            "--profile",
+            "dev",
+            "--region",
+            "us-west-2",
+            "--cluster",
+            "cluster-a",
+            "--analysis-id",
+            "simple-test",
+            "--executing-entity",
+            "johnm",
+            "--dy-command",
+            "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help",
+            "--no-input-staging",
+            "--no-default-activation",
+        ],
+    )
+
+    assert result.exit_code == 0
+    argv = calls["argv"]
+    assert "--no-input-staging" in argv
+    assert "--no-default-activation" in argv
+    assert "--stage-dir" not in argv
+    assert "--run-context-file" not in argv
+
+
 def test_workflow_launch_requires_analysis_identity(monkeypatch) -> None:
     _activate_dayec_runtime(monkeypatch)
 

tests/test_repository_catalog.py

@@ -24,6 +24,7 @@
     / "daylily_available_repositories.yaml"
 )
 UNVALIDATED_COMMAND_IDS = {
+    "simple-test",
     "illumina_run_qc_bclconvert",
     "ultima_snv_alignstats_kitchensink",
     "ont_snv_alignstats_kitchensink",
@@ -204,6 +205,7 @@ def test_repository_catalog_commands_have_run_metadata() -> None:
 
     command_ids = {command.command_id for command in catalog.commands()}
     assert {
+        "simple-test",
         "illumina_snv_alignstats",
         "illumina_snv_alignstats_relatedness_vep_multiqc",
         "illumina_hg002_kitchensink_multiqc",
@@ -452,6 +454,27 @@ def test_repository_catalog_commands_have_run_metadata() -> None:
     assert " -j 125 -p -k" in inflection_bjuice.dy_command
     assert inflection_bjuice.dryrun_dy_command.endswith(" -n")
 
+    simple_test = catalog.get_command("simple-test")
+    assert simple_test.command_class == "utility"
+    assert simple_test.input_contract == "none"
+    assert simple_test.requires_staging is False
+    assert simple_test.requires_run_mount is False
+    assert simple_test.targets == ["help"]
+    assert simple_test.genome == "hg38"
+    assert simple_test.jobs == 1
+    assert simple_test.dy_command == "source dyoainit; dy-a local hg38; dy-r -p -k -j 1 help"
+    assert simple_test.dryrun_dy_command == simple_test.dy_command
+    simple_launch_argv = simple_test.launch_argv(
+        analysis_id="simple-test",
+        executing_entity="johnm",
+    )
+    assert "--dy-command" in simple_launch_argv
+    assert simple_test.dy_command in simple_launch_argv
+    assert "--no-input-staging" in simple_launch_argv
+    assert "--no-default-activation" in simple_launch_argv
+    assert "--stage-dir" not in simple_launch_argv
+    assert "--run-context-file" not in simple_launch_argv
+
 
 def test_repository_catalog_run_analysis_commands_require_run_context() -> None:
     catalog = load_repository_catalog(CATALOG_PATH)