Merge pull request #130 from seqeralabs/edmundmiller/pass-or-fail-stack

fix(report): show failed and cancelled runs in overview

Author: FloWuenne

.nf-core.yml

@@ -0,0 +1,35 @@
+lint:
+  base_config: false
+  files_exist: false
+  files_unchanged: false
+  modules_config: false
+  multiqc_config: false
+  nextflow_config:
+    - custom_config
+    - manifest.homePage
+    - manifest.name
+    - process.cpus
+    - process.memory
+    - process.time
+  pipeline_name_conventions: false
+  schema_lint: false
+  template_strings:
+    - bin/benchmark_report_template.html
+    - assets/AGENTS.md
+  nf_test_content:
+    - tests/nextflow.config
+nf_core_version: 3.3.1
+repository_type: pipeline
+template:
+  author: SciDev Team
+  description: Pipeline to aggregate pertinent metrics across pipeline runs on the Seqera Platform.
+  force: false
+  is_nfcore: false
+  name: nf-aggregate
+  org: seqeralabs
+  outdir: .
+  skip_features:
+    - ci
+    - igenomes
+    - nf_core_configs
+  version: 0.7.0

.prettierignore

@@ -7,5 +7,7 @@ testing/
 testing*
 *.pyc
 bin/
-# Large single-line fixture JSON (Prettier would expand to thousands of lines)
-workflows/nf_aggregate/assets/log_dirs/**/*.json
+**/AGENTS.md
+docs/DESIGN.md
+renovate.json
+workflows/nf_aggregate/assets/log_dirs/

bin/benchmark_report_aggregate.py

@@ -78,24 +78,56 @@ def _is_highlight_process(process: str) -> bool:
     return any(keyword in process_lc for keyword in _HIGHLIGHT_KEYWORDS)
 
 
+def _classify_workflow_status(status: str | None) -> tuple[str, str, bool]:
+    normalized = (status or "").strip().upper()
+    if normalized in {"FAILED", "ERROR", "FAILING"}:
+        return ("Failed", "failed", False)
+    if normalized in {"CANCELLED", "CANCELED", "ABORTED", "ABORT", "STOPPED"}:
+        return ("Cancelled", "cancelled", False)
+    if normalized in {"SUCCEEDED", "SUCCESS", "COMPLETED"}:
+        return ("Succeeded", "success", True)
+    if not normalized:
+        return ("Unknown", "unknown", True)
+    return (normalized.title(), "other", True)
+
+
 def build_report_data(jsonl_dir: Path) -> dict[str, Any]:
     benchmark_overview: list[dict[str, Any]] = []
     run_summary: list[dict[str, Any]] = []
     run_metrics: list[dict[str, Any]] = []
 
     run_cost_acc: dict[tuple[str, str], dict[str, Any]] = {}
     run_pipeline: dict[str, str] = {}
+    included_run_ids: set[str] = set()
 
     for r in _iter_jsonl(jsonl_dir / "runs.jsonl"):
-        benchmark_overview.append({"pipeline": r.get("pipeline"), "group": r.get("group"), "run_id": r.get("run_id")})
-        run_pipeline[str(r.get("run_id", ""))] = str(r.get("pipeline") or "unknown")
+        run_id = str(r.get("run_id", ""))
+        group = str(r.get("group", ""))
+        run_pipeline[run_id] = str(r.get("pipeline") or "unknown")
+        status_label, status_category, report_included = _classify_workflow_status(r.get("status"))
+
+        benchmark_overview.append(
+            {
+                "pipeline": r.get("pipeline"),
+                "group": group,
+                "run_id": run_id,
+                "status": r.get("status"),
+                "status_label": status_label,
+                "status_category": status_category,
+                "report_included": report_included,
+            }
+        )
 
         run_summary.append(
             {
                 "pipeline": r.get("pipeline"),
-                "group": r.get("group"),
-                "run_id": r.get("run_id"),
+                "group": group,
+                "run_id": run_id,
                 "username": r.get("username"),
+                "status": r.get("status"),
+                "status_label": status_label,
+                "status_category": status_category,
+                "report_included": report_included,
                 "Version": r.get("pipeline_version"),
                 "Nextflow_version": r.get("nextflow_version"),
                 "platform_version": r.get("platform_version"),
@@ -110,11 +142,16 @@ def build_report_data(jsonl_dir: Path) -> dict[str, Any]:
             }
         )
 
+        if not report_included:
+            continue
+
+        included_run_ids.add(run_id)
+
         run_metrics.append(
             {
                 "pipeline": r.get("pipeline"),
-                "group": r.get("group"),
-                "run_id": r.get("run_id"),
+                "group": group,
+                "run_id": run_id,
                 "duration": int(r.get("duration_ms") or 0),
                 "cpuTime": _round((float(r.get("cpu_time_ms") or 0) / 1000.0) / 3600.0, 1),
                 "pipeline_runtime": int(r.get("cpu_time_ms") or 0),
@@ -125,7 +162,7 @@ def build_report_data(jsonl_dir: Path) -> dict[str, Any]:
             }
         )
 
-        key = (str(r.get("run_id", "")), str(r.get("group", "")))
+        key = (run_id, group)
         run_cost_acc[key] = {
             "run_id": key[0],
             "group": key[1],
@@ -181,6 +218,9 @@ def build_report_data(jsonl_dir: Path) -> dict[str, Any]:
 
     for t in _iter_jsonl(jsonl_dir / "tasks.jsonl"):
         run_id = str(t.get("run_id", ""))
+        if run_id not in included_run_ids:
+            continue
+
         group = str(t.get("group", ""))
         process = str(t.get("process", ""))
         process_short = str(t.get("process_short", ""))