Merge distributed pipeline hardening

.github/workflows/python.yml

@@ -0,0 +1,28 @@
+name: python
+
+on:
+  push:
+    paths:
+      - "scimesh/**"
+      - "tests/**"
+      - "pyproject.toml"
+      - ".github/workflows/python.yml"
+  pull_request:
+    paths:
+      - "scimesh/**"
+      - "tests/**"
+      - "pyproject.toml"
+      - ".github/workflows/python.yml"
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+          cache: pip
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install -e '.[dev]'
+      - run: pytest -q

.gitignore

@@ -11,3 +11,7 @@ results/
 *_similarities.csv
 test_results.csv
 test_structures/
+
+# Local coordinator-worker execution state
+worker-data*/
+scimesh-worker-data/

README.md

@@ -1,11 +1,12 @@
 # SciMesh
 
 SciMesh is a scientific-workload framework for molecular datasets. Its public CLI
-currently runs exact similarity search and sparse similarity-graph construction
+runs exact similarity search and sparse similarity-graph construction locally in
-locally in one Python process; it creates no dense similarity matrix. A Python
+one Python process; it creates no dense similarity matrix. The Go/PostgreSQL
-Worker client and the planned Go/PostgreSQL coordinator contract are tracked in
+coordinator and Python worker can run a diagnostic, shard-based
-the repository, but distributed execution is not available yet; see
+`similarity-search` pipeline locally. Its CSV artifacts are not a global result
-[`STATUS.md`](STATUS.md).
+until CTX-07--09 add planning and reduction; use the local CLI for scientific
+results today. See [`STATUS.md`](STATUS.md).
 
 The ChEMBL TSV database is intentionally not included in this repository. Download it separately and pass its path to the commands below. The expected columns are `chembl_id` and `canonical_smiles`.
 

STATUS.md

@@ -36,7 +36,7 @@ Docker PostgreSQL stack on 2026-07-23.
 | CTX-08 Distributed similarity-search | Not started | Local reference exists. |
 | CTX-09 Reducer and final-result API | Not started | Depends on CTX-07 and CTX-08. |
 | CTX-10 Distributed similarity-graph | Not started | Local reference exists. |
-| CTX-11 Dashboard/operator view | In progress | `feat/web-interface` adds a protected local view: job/task/worker status, dataset upload, diagnostic partial-artifact download, and polling. Final-result reduction remains CTX-09. |
+| CTX-11 Dashboard/operator view | Implemented (diagnostic scope) | Protected local view: job/task/worker status, validated similarity-search upload, diagnostic partial-artifact download, and bounded polling. Final-result reduction remains CTX-09. |
 | CTX-12 Reliability, security, CI | In progress | Unit, race, PostgreSQL integration, and smoke checks exist; CI hardening remains. |
 
 ## Next recommended assignment
@@ -53,6 +53,9 @@ reduction boundaries before implementing distributed search or graph execution.
   names and hyphenated CLI names while the contract is consolidated.
 - A real-stack worker test uses a small `query_smiles` shard. Resolving a
   `query_id` once and sharing it across shards belongs to CTX-07.
+- The coordinator accepts uploaded distributed jobs only for
+  `similarity-search` with `query_smiles`. It rejects `similarity-graph` until
+  CTX-10 supplies cross-shard pair planning.
 
 ## Update rule
 

coordinator/cmd/coordinator/main.go

@@ -71,14 +71,14 @@ func run() error {
 	useCases := httptransport.UseCases{
 		RegisterWorker:   usecase.NewRegisterWorker(workerRepo, clk),
 		CreateJob:        usecase.NewCreateJob(jobRepo, taskRepo, tx, clk),
-		SubmitDataset:    usecase.NewSubmitDataset(blobStore, artifactRepo, jobRepo, taskRepo, tx, clk),
+		SubmitDataset:    usecase.NewSubmitDataset(blobStore, artifactRepo, jobRepo, taskRepo, tx, clk, cfg.DefaultMaxAttempts),
-		ClaimTask:        usecase.NewClaimTask(taskRepo, clk, cfg.LeaseDuration),
+		ClaimTask:        usecase.NewClaimTask(taskRepo, jobRepo, workerRepo, tx, clk, cfg.LeaseDuration),
 		RenewLease:       usecase.NewRenewLease(taskRepo, workerRepo, tx, clk, cfg.LeaseDuration),
 		CompleteTask:     usecase.NewCompleteTask(taskRepo, jobRepo, artifactRepo, tx, clk),
 		FailTask:         usecase.NewFailTask(taskRepo, jobRepo, tx, clk),
 		GetJobStatus:     usecase.NewGetJobStatus(jobRepo, taskRepo),
 		CancelJob:        usecase.NewCancelJob(jobRepo, taskRepo, tx, clk),
-		UploadArtifact:   usecase.NewUploadArtifact(taskRepo, artifactRepo, blobStore, clk),
+		UploadArtifact:   usecase.NewUploadArtifact(taskRepo, artifactRepo, blobStore, tx, clk),
 		DownloadArtifact: usecase.NewDownloadArtifact(artifactRepo, blobStore),
 		GetTaskInput:     usecase.NewGetTaskInput(taskRepo, artifactRepo, blobStore),
 		Dashboard:        usecase.NewDashboard(uiReadRepo),
@@ -87,7 +87,7 @@ func run() error {
 	// Background reapers are tracked so shutdown can wait for them. Without this
 	// the process would exit mid-UPDATE, and the deferred pool.Close() would pull
 	// connections out from under them.
-	expireLeases := usecase.NewExpireLeases(taskRepo, clk)
+	expireLeases := usecase.NewExpireLeases(taskRepo, jobRepo, tx, clk)
 	markOffline := usecase.NewMarkWorkersOffline(workerRepo, clk, cfg.WorkerOfflineAfter)
 
 	var wg sync.WaitGroup

coordinator/internal/chunk/tsv.go

@@ -7,12 +7,19 @@ import (
 	"bytes"
 	"fmt"
 	"io"
+	"strings"
 )
 
 // ErrNoRows is returned when the input has a header but no data rows: a job with
 // zero tasks could never complete, so it is rejected at the source.
 var ErrNoRows = fmt.Errorf("input has no data rows")
 
+// maxShardBytes bounds the coordinator memory used by one in-progress shard.
+// The uploaded file may be much larger: it is first stored on disk, then split
+// in small bounded pieces. Operators can lower rowsPerShard when this limit is
+// reached rather than exhausting the coordinator process.
+const maxShardBytes = 64 << 20 // 64 MiB
+
 // SplitTSV reads a header-plus-rows text stream and cuts it into shards of at
 // most rowsPerShard data rows. Every shard repeats the header, so a worker can
 // parse its shard in isolation. emit is called once per shard, in order, with a
@@ -26,13 +33,25 @@ var ErrNoRows = fmt.Errorf("input has no data rows")
 // Only one shard is buffered at a time, so memory is bounded by shard size (a
 // worker-sized slice of the data), not by the size of the whole dataset.
 func SplitTSV(r io.Reader, rowsPerShard int, emit func(index int, shard io.Reader) error) error {
-	return SplitTSVLimit(r, rowsPerShard, 0, emit)
+	return splitTSVLimit(r, rowsPerShard, 0, nil, emit)
 }
 
 // SplitTSVLimit behaves like SplitTSV but emits no more than maxRows data rows.
 // A maxRows value of zero means unlimited. This lets an operator make a small,
 // representative pipeline check without materialising a second dataset file.
 func SplitTSVLimit(r io.Reader, rowsPerShard, maxRows int, emit func(index int, shard io.Reader) error) error {
+	return splitTSVLimit(r, rowsPerShard, maxRows, nil, emit)
+}
+
+// SplitChEMBLTSVLimit is the coordinator's scientific-upload splitter. It
+// validates the two columns every local SciMesh workload requires before any
+// shard task is persisted, while generic SplitTSV remains reusable for future
+// non-chemistry workloads.
+func SplitChEMBLTSVLimit(r io.Reader, rowsPerShard, maxRows int, emit func(index int, shard io.Reader) error) error {
+	return splitTSVLimit(r, rowsPerShard, maxRows, validateChEMBLHeader, emit)
+}
+
+func splitTSVLimit(r io.Reader, rowsPerShard, maxRows int, validateHeader func([]byte) error, emit func(index int, shard io.Reader) error) error {
 	if rowsPerShard <= 0 {
 		return fmt.Errorf("rowsPerShard must be positive, got %d", rowsPerShard)
 	}
@@ -51,6 +70,11 @@ func SplitTSVLimit(r io.Reader, rowsPerShard, maxRows int, emit func(index int,
 		return ErrNoRows // completely empty input
 	}
 	header := append([]byte(nil), sc.Bytes()...)
+	if validateHeader != nil {
+		if err := validateHeader(header); err != nil {
+			return err
+		}
+	}
 
 	var (
 		buf   bytes.Buffer
@@ -71,9 +95,15 @@ func SplitTSVLimit(r io.Reader, rowsPerShard, maxRows int, emit func(index int,
 
 	for sc.Scan() {
 		if rows == 0 {
+			if len(header)+1 > maxShardBytes {
+				return fmt.Errorf("TSV header exceeds maximum shard size of %d bytes", maxShardBytes)
+			}
 			buf.Write(header)
 			buf.WriteByte('\n')
 		}
+		if buf.Len()+len(sc.Bytes())+1 > maxShardBytes {
+			return fmt.Errorf("shard exceeds maximum size of %d bytes; lower rowsPerShard", maxShardBytes)
+		}
 		buf.Write(sc.Bytes())
 		buf.WriteByte('\n')
 		rows++
@@ -103,3 +133,17 @@ func SplitTSVLimit(r io.Reader, rowsPerShard, maxRows int, emit func(index int,
 	}
 	return nil
 }
+
+func validateChEMBLHeader(header []byte) error {
+	seen := make(map[string]struct{})
+	for _, field := range strings.Split(strings.TrimPrefix(string(header), "\ufeff"), "\t") {
+		seen[field] = struct{}{}
+	}
+	if _, ok := seen["chembl_id"]; !ok {
+		return fmt.Errorf("TSV is missing required column chembl_id")
+	}
+	if _, ok := seen["canonical_smiles"]; !ok {
+		return fmt.Errorf("TSV is missing required column canonical_smiles")
+	}
+	return nil
+}

coordinator/internal/chunk/tsv_test.go

@@ -119,6 +119,14 @@ func TestSplitLimitUsesOnlyLeadingDataRows(t *testing.T) {
 	}
 }
 
+func TestChEMBLSplitRejectsMissingRequiredColumns(t *testing.T) {
+	err := SplitChEMBLTSVLimit(strings.NewReader("id\tsmiles\nA\tCC\n"), 1, 0,
+		func(int, io.Reader) error { return nil })
+	if err == nil || !strings.Contains(err.Error(), "chembl_id") {
+		t.Errorf("err = %v, want missing-column error", err)
+	}
+}
+
 // The scanned bytes are reused by bufio; the shard buffer must copy them, or a
 // later row would corrupt an earlier one. This guards that copy.
 func TestSplitDoesNotAliasScannerBuffer(t *testing.T) {

coordinator/internal/infra/config.go

@@ -129,6 +129,9 @@ func LoadConfig() (Config, error) {
 	if cfg.DefaultMaxAttempts, err = getEnvInt("DEFAULT_MAX_ATTEMPTS", cfg.DefaultMaxAttempts); err != nil {
 		return Config{}, err
 	}
+	if cfg.DefaultMaxAttempts < 1 {
+		return Config{}, fmt.Errorf("DEFAULT_MAX_ATTEMPTS must be positive")
+	}
 
 	return cfg, nil
 }

coordinator/internal/infra/config_test.go

@@ -32,3 +32,14 @@ func TestLoadConfigAllowsDistinctUIAndWorkerTokens(t *testing.T) {
 		t.Fatalf("unexpected tokens: %+v", cfg)
 	}
 }
+
+func TestLoadConfigRejectsNonPositiveDefaultMaxAttempts(t *testing.T) {
+	t.Setenv("ENV_FILE", filepath.Join(t.TempDir(), "missing.env"))
+	t.Setenv("DATABASE_URL", "postgres://test")
+	t.Setenv("DEFAULT_MAX_ATTEMPTS", "0")
+
+	_, err := LoadConfig()
+	if err == nil || !strings.Contains(err.Error(), "DEFAULT_MAX_ATTEMPTS") {
+		t.Fatalf("LoadConfig error = %v, want default-attempt validation", err)
+	}
+}

coordinator/internal/memstore/memstore.go

@@ -160,17 +160,18 @@ func (r *TaskRepo) CancelByJob(_ context.Context, jobID uuid.UUID, now time.Time
 	return cancelled, nil
 }
 
-func (r *TaskRepo) ExpireLeases(ctx context.Context, now time.Time) (int64, error) {
+func (r *TaskRepo) ExpireLeases(ctx context.Context, now time.Time) ([]uuid.UUID, error) {
 	r.mu.Lock()
 	defer r.mu.Unlock()
-	var n int64
+	affected := make([]uuid.UUID, 0)
 	for _, t := range r.tasks {
-		if t.Status == domain.TaskLeased && t.LeaseExpiresAt != nil && t.LeaseExpiresAt.Before(now) {
+		if (t.Status == domain.TaskLeased || t.Status == domain.TaskRunning) &&
+			t.LeaseExpiresAt != nil && t.LeaseExpiresAt.Before(now) {
 			t.ExpireLease(now)
-			n++
+			affected = append(affected, t.JobID)
 		}
 	}
-	return n, nil
+	return affected, nil
 }
 
 // --- JobRepo -------------------------------------------------------------
@@ -298,6 +299,23 @@ func (r *ArtifactRepo) Get(ctx context.Context, id uuid.UUID) (*domain.Artifact,
 	return &cp, nil
 }
 
+func (r *ArtifactRepo) FindPartialResult(_ context.Context, taskID uuid.UUID, attempt int) (*domain.Artifact, error) {
+	r.mu.Lock()
+	defer r.mu.Unlock()
+	for _, a := range r.arts {
+		if a.TaskID != nil && *a.TaskID == taskID && a.Kind == domain.ArtifactPartialResult &&
+			a.Attempt != nil && *a.Attempt == attempt {
+			return cloneArtifact(a), nil
+		}
+	}
+	return nil, nil
+}
+
+func cloneArtifact(a *domain.Artifact) *domain.Artifact {
+	cp := *a
+	return &cp
+}
+
 // --- BlobStore -----------------------------------------------------------
 
 type BlobStore struct {

coordinator/internal/memstore/ui_read.go

@@ -60,6 +60,18 @@ func (r *UIReadRepo) ListTasksByJob(_ context.Context, jobID uuid.UUID) ([]domai
 	sort.Slice(out, func(i, j int) bool { return out[i].ChunkIndex < out[j].ChunkIndex })
 	return out, nil
 }
+
+func (r *UIReadRepo) ListTasksByJobs(ctx context.Context, jobIDs []uuid.UUID) (map[uuid.UUID][]domain.Task, error) {
+	out := make(map[uuid.UUID][]domain.Task, len(jobIDs))
+	for _, id := range jobIDs {
+		tasks, err := r.ListTasksByJob(ctx, id)
+		if err != nil {
+			return nil, err
+		}
+		out[id] = tasks
+	}
+	return out, nil
+}
 func (r *UIReadRepo) ListWorkers(_ context.Context, limit int) ([]domain.Worker, error) {
 	if limit < 1 || limit > 100 {
 		return nil, domain.ErrInvalidInput

coordinator/internal/storage/postgres/artifact_repo.go

@@ -70,3 +70,33 @@ func (r *ArtifactRepo) Get(ctx context.Context, id uuid.UUID) (*domain.Artifact,
 	a.Kind = domain.ArtifactKind(kind)
 	return &a, nil
 }
+
+func (r *ArtifactRepo) FindPartialResult(ctx context.Context, taskID uuid.UUID, attempt int) (*domain.Artifact, error) {
+	sql, args, err := psql.Select(artifactColumns...).
+		From("artifacts").
+		Where(sq.Eq{
+			"task_id": taskID,
+			"attempt": attempt,
+			"kind":    string(domain.ArtifactPartialResult),
+		}).
+		ToSql()
+	if err != nil {
+		return nil, err
+	}
+
+	var (
+		a    domain.Artifact
+		kind string
+	)
+	err = conn(ctx, r.pool).QueryRow(ctx, sql, args...).Scan(
+		&a.ID, &a.JobID, &a.TaskID, &a.Attempt, &kind, &a.Filename, &a.StorageKey,
+		&a.ContentType, &a.SizeBytes, &a.SHA256, &a.CreatedAt)
+	if errors.Is(err, pgx.ErrNoRows) {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, fmt.Errorf("find partial result: %w", err)
+	}
+	a.Kind = domain.ArtifactKind(kind)
+	return &a, nil
+}

coordinator/internal/storage/postgres/integration_test.go

@@ -360,12 +360,23 @@ func TestCompleteTaskReplayIsIdempotent(t *testing.T) {
 		t.Errorf("replay must be idempotent, got %v", err)
 	}
 
-	// A different result artifact for the same task is a genuine conflict.
+}
-	art2 := seedArtifact(t, pool, job.ID, &claimed.ID, domain.ArtifactPartialResult)
+
-	other := in
+func TestPartialResultIsUniquePerTaskAttempt(t *testing.T) {
-	other.ResultArtifactID = art2.ID
+	pool := testPool(t)
-	if _, err := uc.Execute(ctx, other); !errors.Is(err, domain.ErrResultConflict) {
+	ctx := context.Background()
-		t.Errorf("err = %v, want ErrResultConflict", err)
+	job, tasks := seedJob(t, pool, 1)
+	taskID := tasks[0].ID
+	first := seedArtifact(t, pool, job.ID, &taskID, domain.ArtifactPartialResult)
+	second, err := domain.NewArtifact(job.ID, &taskID, domain.ArtifactPartialResult, "retry.csv", "text/csv", time.Now().UTC())
+	if err != nil {
+		t.Fatal(err)
+	}
+	attempt := 1
+	second.Attempt = &attempt
+	second.SetContent("other-sha", 5)
+	if err := NewArtifactRepo(pool).Insert(ctx, second); err == nil {
+		t.Fatalf("second partial artifact for %s/%d was accepted after %s", taskID, attempt, first.ID)
 	}
 }
 

coordinator/internal/storage/postgres/task_repo.go

@@ -337,17 +337,26 @@ SET status           = CASE WHEN attempt < max_attempts THEN 'pending'::task_sta
                             ELSE error_message END,
     completed_at     = CASE WHEN attempt >= max_attempts THEN $1 ELSE completed_at END,
     version          = version + 1
-WHERE status IN ('leased','running') AND lease_expires_at < $1`
+WHERE status IN ('leased','running') AND lease_expires_at < $1
+RETURNING job_id`
 
-func (r *TaskRepo) ExpireLeases(ctx context.Context, now time.Time) (int64, error) {
+func (r *TaskRepo) ExpireLeases(ctx context.Context, now time.Time) ([]uuid.UUID, error) {
-	var affected int64
+	var affected []uuid.UUID
 	err := withRetry(ctx, func(ctx context.Context) error {
-		tag, err := conn(ctx, r.pool).Exec(ctx, expireLeasesSQL, now, domain.ErrCodeLeaseExpired)
+		rows, err := conn(ctx, r.pool).Query(ctx, expireLeasesSQL, now, domain.ErrCodeLeaseExpired)
 		if err != nil {
 			return err
 		}
-		affected = tag.RowsAffected()
+		defer rows.Close()
-		return nil
+		affected = affected[:0]
+		for rows.Next() {
+			var jobID uuid.UUID
+			if err := rows.Scan(&jobID); err != nil {
+				return err
+			}
+			affected = append(affected, jobID)
+		}
+		return rows.Err()
 	})
 	return affected, err
 }

coordinator/internal/storage/postgres/ui_read_repo.go

@@ -75,6 +75,31 @@ func (r *UIReadRepo) ListTasksByJob(ctx context.Context, jobID uuid.UUID) ([]dom
 	return tasks, rows.Err()
 }
 
+func (r *UIReadRepo) ListTasksByJobs(ctx context.Context, jobIDs []uuid.UUID) (map[uuid.UUID][]domain.Task, error) {
+	out := make(map[uuid.UUID][]domain.Task, len(jobIDs))
+	if len(jobIDs) == 0 {
+		return out, nil
+	}
+	sql, args, err := psql.Select(taskColumns...).From("tasks").
+		Where(sq.Eq{"job_id": jobIDs}).OrderBy("job_id ASC", "chunk_index ASC").ToSql()
+	if err != nil {
+		return nil, err
+	}
+	rows, err := conn(ctx, r.pool).Query(ctx, sql, args...)
+	if err != nil {
+		return nil, fmt.Errorf("list tasks by jobs: %w", err)
+	}
+	defer rows.Close()
+	for rows.Next() {
+		task, err := scanTask(rows)
+		if err != nil {
+			return nil, err
+		}
+		out[task.JobID] = append(out[task.JobID], *task)
+	}
+	return out, rows.Err()
+}
+
 func (r *UIReadRepo) ListWorkers(ctx context.Context, limit int) ([]domain.Worker, error) {
 	if limit < 1 || limit > 100 {
 		return nil, domain.ErrInvalidInput

coordinator/internal/transport/http/handlers.go

@@ -79,6 +79,10 @@ func (s *Server) handleClaim(w http.ResponseWriter, r *http.Request) {
 		s.writeError(w, r, domain.ErrInvalidInput)
 		return
 	}
+	if _, err := uuid.Parse(req.WorkerID); err != nil {
+		s.writeError(w, r, domain.ErrInvalidInput)
+		return
+	}
 
 	claimed, err := s.uc.ClaimTask.Execute(ctx, usecase.ClaimTaskInput{
 		WorkerID:  req.WorkerID,

coordinator/internal/transport/http/server_test.go

@@ -23,8 +23,9 @@ const token = "secret"
 const uiToken = "ui-secret"
 
 type env struct {
-	ts    *httptest.Server
+	ts       *httptest.Server
-	blobs *memstore.BlobStore
+	blobs    *memstore.BlobStore
+	workerID string
 }
 
 func newEnv(t *testing.T, ready func(context.Context) error) *env {
@@ -45,22 +46,28 @@ func newEnvWithUIToken(t *testing.T, ready func(context.Context) error, configur
 	uc := coordhttp.UseCases{
 		RegisterWorker:   usecase.NewRegisterWorker(work, clk),
 		CreateJob:        usecase.NewCreateJob(jobs, tasks, tx, clk),
-		SubmitDataset:    usecase.NewSubmitDataset(blobs, arts, jobs, tasks, tx, clk),
+		SubmitDataset:    usecase.NewSubmitDataset(blobs, arts, jobs, tasks, tx, clk, 3),
-		ClaimTask:        usecase.NewClaimTask(tasks, clk, lease),
+		ClaimTask:        usecase.NewClaimTask(tasks, jobs, work, tx, clk, lease),
 		RenewLease:       usecase.NewRenewLease(tasks, work, tx, clk, lease),
 		CompleteTask:     usecase.NewCompleteTask(tasks, jobs, arts, tx, clk),
 		FailTask:         usecase.NewFailTask(tasks, jobs, tx, clk),
 		GetJobStatus:     usecase.NewGetJobStatus(jobs, tasks),
 		CancelJob:        usecase.NewCancelJob(jobs, tasks, tx, clk),
-		UploadArtifact:   usecase.NewUploadArtifact(tasks, arts, blobs, clk),
+		UploadArtifact:   usecase.NewUploadArtifact(tasks, arts, blobs, tx, clk),
 		DownloadArtifact: usecase.NewDownloadArtifact(arts, blobs),
 		GetTaskInput:     usecase.NewGetTaskInput(tasks, arts, blobs),
 		Dashboard:        usecase.NewDashboard(memstore.NewUIReadRepo(jobs, tasks, work, arts)),
 	}
+	worker, err := uc.RegisterWorker.Execute(context.Background(), usecase.RegisterWorkerInput{
+		Name: "test-worker", Capabilities: []string{"w", "similarity-search"},
+	})
+	if err != nil {
+		t.Fatalf("register test worker: %v", err)
+	}
 	srv := coordhttp.NewServer(uc, slog.New(slog.NewTextHandler(io.Discard, nil)), 5*time.Second, 15*time.Second, 1<<30, ready)
 	ts := httptest.NewServer(srv.Handler(token, configuredUIToken))
 	t.Cleanup(ts.Close)
-	return &env{ts: ts, blobs: blobs}
+	return &env{ts: ts, blobs: blobs, workerID: worker.ID.String()}
 }
 
 func healthy(context.Context) error { return nil }
@@ -68,6 +75,7 @@ func healthy(context.Context) error { return nil }
 // do sends an authenticated JSON request and returns status + decoded body.
 func (e *env) do(t *testing.T, method, path, body string) (int, map[string]any) {
 	t.Helper()
+	body = strings.ReplaceAll(body, `"worker_id":"w1"`, `"worker_id":"`+e.workerID+`"`)
 	req, _ := http.NewRequestWithContext(context.Background(), method, e.ts.URL+path, strings.NewReader(body))
 	req.Header.Set("Authorization", "Bearer "+token)
 	if body != "" {
@@ -330,6 +338,26 @@ func TestRegisterRejectsNoCapabilities(t *testing.T) {
 	}
 }
 
+func TestClaimRequiresRegisteredWorkerAndUsesStoredCapabilities(t *testing.T) {
+	e := newEnv(t, healthy)
+	if code, _ := e.do(t, "POST", "/tasks/claim", `{"worker_id":"not-a-uuid"}`); code != http.StatusBadRequest {
+		t.Fatalf("invalid worker id claim = %d, want 400", code)
+	}
+	if code, _ := e.do(t, "POST", "/tasks/claim", `{"worker_id":"11111111-1111-4111-8111-111111111111"}`); code != http.StatusNotFound {
+		t.Fatalf("unregistered worker claim = %d, want 404", code)
+	}
+	if code, _ := e.do(t, "POST", "/jobs", `{"workload":"w","input_uri":"s3://in","chunks":[{"chunk_index":0,"input_uri":"s3://c","input_sha256":"sha"}]}`); code != http.StatusCreated {
+		t.Fatalf("create job = %d", code)
+	}
+	code, worker := e.do(t, "POST", "/workers/register", `{"name":"search-only","capabilities":["similarity-search"]}`)
+	if code != http.StatusCreated {
+		t.Fatalf("register = %d", code)
+	}
+	if code, _ := e.do(t, "POST", "/tasks/claim", `{"worker_id":"`+worker["worker_id"].(string)+`","capabilities":["w"]}`); code != http.StatusNoContent {
+		t.Fatalf("forged capability claim = %d, want 204", code)
+	}
+}
+
 func TestFullLifecycle(t *testing.T) {
 	e := newEnv(t, healthy)
 
@@ -393,9 +421,9 @@ func TestForeignArtifactResultConflict(t *testing.T) {
 
 func TestUploadDatasetChunksAndServesInput(t *testing.T) {
 	e := newEnv(t, healthy)
-	tsv := "id\tsmiles\nA\tCC\nB\tCCC\nC\tCCCC\nD\tCCCCC\nE\tCCCCCC\n"
+	tsv := "chembl_id\tcanonical_smiles\nA\tCC\nB\tCCC\nC\tCCCC\nD\tCCCCC\nE\tCCCCCC\n"
 
-	code, body := e.uploadDataset(t, "w", 2, tsv)
+	code, body := e.uploadDataset(t, "similarity-search", 2, tsv)
 	if code != 201 {
 		t.Fatalf("upload: status = %d", code)
 	}
@@ -421,7 +449,7 @@ func TestUploadDatasetChunksAndServesInput(t *testing.T) {
 		t.Fatalf("get input: status = %d", resp.StatusCode)
 	}
 	shard, _ := io.ReadAll(resp.Body)
-	if !strings.HasPrefix(string(shard), "id\tsmiles\n") {
+	if !strings.HasPrefix(string(shard), "chembl_id\tcanonical_smiles\n") {
 		t.Errorf("shard missing header: %q", shard)
 	}
 }
@@ -430,11 +458,12 @@ func TestUploadDatasetLimitsRows(t *testing.T) {
 	e := newEnv(t, healthy)
 	var buf bytes.Buffer
 	mw := multipart.NewWriter(&buf)
-	_ = mw.WriteField("workload", "w")
+	_ = mw.WriteField("workload", "similarity-search")
+	_ = mw.WriteField("parameters", `{"query_smiles":"CCO"}`)
 	_ = mw.WriteField("chunk_rows", "2")
 	_ = mw.WriteField("max_rows", "3")
 	fw, _ := mw.CreateFormFile("file", "chembl.tsv")
-	_, _ = io.Copy(fw, strings.NewReader("id\tsmiles\nA\tCC\nB\tCCC\nC\tCCCC\nD\tCCCCC\n"))
+	_, _ = io.Copy(fw, strings.NewReader("chembl_id\tcanonical_smiles\nA\tCC\nB\tCCC\nC\tCCCC\nD\tCCCCC\n"))
 	_ = mw.Close()
 	req, _ := http.NewRequestWithContext(context.Background(), "POST", e.ts.URL+"/jobs/upload", &buf)
 	req.Header.Set("Authorization", "Bearer "+token)
@@ -451,6 +480,29 @@ func TestUploadDatasetLimitsRows(t *testing.T) {
 	}
 }
 
+func TestUploadDatasetRejectsMissingChEMBLColumns(t *testing.T) {
+	e := newEnv(t, healthy)
+	var buf bytes.Buffer
+	mw := multipart.NewWriter(&buf)
+	_ = mw.WriteField("workload", "similarity-search")
+	_ = mw.WriteField("parameters", `{"query_smiles":"CCO"}`)
+	_ = mw.WriteField("chunk_rows", "2")
+	fw, _ := mw.CreateFormFile("file", "not-chembl.tsv")
+	_, _ = io.Copy(fw, strings.NewReader("id\tsmiles\nA\tCC\n"))
+	_ = mw.Close()
+	req, _ := http.NewRequestWithContext(context.Background(), "POST", e.ts.URL+"/jobs/upload", &buf)
+	req.Header.Set("Authorization", "Bearer "+token)
+	req.Header.Set("Content-Type", mw.FormDataContentType())
+	resp, err := http.DefaultClient.Do(req)
+	if err != nil {
+		t.Fatal(err)
+	}
+	defer resp.Body.Close()
+	if resp.StatusCode != http.StatusBadRequest {
+		t.Errorf("missing ChEMBL columns = %d, want 400", resp.StatusCode)
+	}
+}
+
 func TestErrorMappings(t *testing.T) {
 	e := newEnv(t, healthy)
 	zero := "00000000-0000-0000-0000-000000000000"
@@ -478,10 +530,11 @@ func TestUploadDatasetRejectsAmbiguousMultipartInput(t *testing.T) {
 	e := newEnv(t, healthy)
 	var buf bytes.Buffer
 	mw := multipart.NewWriter(&buf)
-	_ = mw.WriteField("workload", "w")
+	_ = mw.WriteField("workload", "similarity-search")
+	_ = mw.WriteField("parameters", `{"query_smiles":"CCO"}`)
 	_ = mw.WriteField("chunk_rows", "not-a-number")
 	fw, _ := mw.CreateFormFile("file", "chembl.tsv")
-	_, _ = io.Copy(fw, strings.NewReader("id\tsmiles\nA\tCC\n"))
+	_, _ = io.Copy(fw, strings.NewReader("chembl_id\tcanonical_smiles\nA\tCC\n"))
 	_ = mw.Close()
 
 	req, _ := http.NewRequestWithContext(context.Background(), "POST", e.ts.URL+"/jobs/upload", &buf)
@@ -505,6 +558,9 @@ func (e *env) putArtifact(t *testing.T, taskID, worker string, attempt int, data
 		e.ts.URL+"/tasks/"+taskID+"/artifacts/r.csv", strings.NewReader(data))
 	req.Header.Set("Authorization", "Bearer "+token)
 	req.Header.Set("Content-Type", "text/csv")
+	if worker == "w1" {
+		worker = e.workerID
+	}
 	req.Header.Set("X-Worker-ID", worker)
 	req.Header.Set("X-Task-Attempt", itoa(attempt))
 	resp, err := http.DefaultClient.Do(req)
@@ -526,6 +582,7 @@ func (e *env) uploadDataset(t *testing.T, workload string, rows int, tsv string)
 	var buf bytes.Buffer
 	mw := multipart.NewWriter(&buf)
 	_ = mw.WriteField("workload", workload)
+	_ = mw.WriteField("parameters", `{"query_smiles":"CCO"}`)
 	_ = mw.WriteField("chunk_rows", itoa(rows))
 	fw, _ := mw.CreateFormFile("file", "chembl.tsv")
 	_, _ = io.Copy(fw, strings.NewReader(tsv))

coordinator/internal/transport/http/templates/job.html

@@ -22,7 +22,7 @@
   <script>
     const id={{printf "%q" .ID}},state={pending:['Waiting for a worker','waiting','Waiting for an available worker with the required capability.'],leased:['Assigned to a worker','active','A worker has claimed the task and should begin processing shortly.'],running:['Running','active','A worker is reading a shard, calculating fingerprints, and uploading its result through the coordinator.'],completed:['Tasks complete','success','Every shard task is complete. Files below are still partial results.'],failed:['Needs attention','danger','One or more shard tasks failed. Open the task list below for details.'],cancelled:['Stopped','waiting','The operator stopped this job. No new shards can be claimed.']};
     const stop=document.querySelector('#stop-job');if(stop)stop.addEventListener('click',async()=>{if(!confirm('Stop this job? Unfinished shards will be cancelled.'))return;stop.disabled=true;const response=await fetch('/ui/api/jobs/'+id+'/cancel',{method:'POST'});if(!response.ok){stop.disabled=false;alert('Unable to stop this job.');return}location.reload()});
-    setInterval(async()=>{try{const response=await fetch('/ui/api/jobs/'+id);if(!response.ok)return;const job=await response.json(),info=state[job.status]||[job.status,'waiting','Status reported by the coordinator.'],done=job.completed+job.failed+job.cancelled,percent=job.total?Math.min(100,Math.floor(done*100/job.total)):0,badge=document.querySelector('#status');badge.textContent=info[0];badge.className='status status-'+info[1];document.querySelector('#hint').textContent=info[2];document.querySelector('#progress').textContent=job.completed+' of '+job.total+' tasks complete'+(job.failed?' · failed: '+job.failed:'')+(job.cancelled?' · stopped: '+job.cancelled:'');document.querySelector('#progress-bar').style.width=percent+'%';for(const key of ['total','completed','pending','failed','cancelled'])document.querySelector('#'+key).textContent=job[key];document.querySelector('#active').textContent=job.leased+job.running}catch(_){}} ,2000);
+    const terminal=new Set(['completed','failed','cancelled']);let timer;const poll=async()=>{try{const response=await fetch('/ui/api/jobs/'+id);if(!response.ok)return;const job=await response.json(),info=state[job.status]||[job.status,'waiting','Status reported by the coordinator.'],done=job.completed+job.failed+job.cancelled,percent=job.total?Math.min(100,Math.floor(done*100/job.total)):0,badge=document.querySelector('#status');badge.textContent=info[0];badge.className='status status-'+info[1];document.querySelector('#hint').textContent=info[2];document.querySelector('#progress').textContent=job.completed+' of '+job.total+' tasks complete'+(job.failed?' · failed: '+job.failed:'')+(job.cancelled?' · stopped: '+job.cancelled:'');document.querySelector('#progress-bar').style.width=percent+'%';for(const key of ['total','completed','pending','failed','cancelled'])document.querySelector('#'+key).textContent=job[key];document.querySelector('#active').textContent=job.leased+job.running;if(terminal.has(job.status)&&timer){clearInterval(timer);timer=undefined}}catch(_){}};const start=()=>{if(!timer&&!document.hidden&&!terminal.has(document.querySelector('#status').textContent.toLowerCase()))timer=setInterval(poll,2000)};document.addEventListener('visibilitychange',()=>{if(document.hidden&&timer){clearInterval(timer);timer=undefined}else start()});start();
   </script>
 </body>
 </html>

coordinator/internal/usecase/artifact.go

@@ -14,12 +14,13 @@ type UploadArtifact struct {
 	tasks     TaskRepository
 	artifacts ArtifactRepository
 	blobs     BlobStore
+	tx        TxManager
 	clk       Clock
 }
 
 func NewUploadArtifact(tasks TaskRepository, artifacts ArtifactRepository,
-	blobs BlobStore, clk Clock) *UploadArtifact {
+	blobs BlobStore, tx TxManager, clk Clock) *UploadArtifact {
-	return &UploadArtifact{tasks: tasks, artifacts: artifacts, blobs: blobs, clk: clk}
+	return &UploadArtifact{tasks: tasks, artifacts: artifacts, blobs: blobs, tx: tx, clk: clk}
 }
 
 func (uc *UploadArtifact) Execute(ctx context.Context, in UploadArtifactInput) (*domain.Artifact, error) {
@@ -32,6 +33,15 @@ func (uc *UploadArtifact) Execute(ctx context.Context, in UploadArtifactInput) (
 	if !task.IsLeaseHeldBy(in.WorkerID, in.Attempt, uc.clk.Now()) {
 		return nil, domain.ErrLeaseConflict
 	}
+	// A client can retry a PUT after losing the response. Return the one durable
+	// result for this lease attempt instead of storing duplicate artifacts.
+	existing, err := uc.artifacts.FindPartialResult(ctx, in.TaskID, in.Attempt)
+	if err != nil {
+		return nil, err
+	}
+	if existing != nil {
+		return existing, nil
+	}
 
 	taskID := task.ID
 	art, err := domain.NewArtifact(task.JobID, &taskID, domain.ArtifactPartialResult,
@@ -50,25 +60,41 @@ func (uc *UploadArtifact) Execute(ctx context.Context, in UploadArtifactInput) (
 	}
 	art.SetContent(sum, size)
 
-	// The stream may take longer than the lease. Re-check after it finishes so
+	// The stream may take longer than the lease. Lock the task while re-checking
-	// an expired worker cannot leave a durable result record behind. Completion
+	// ownership and inserting metadata: completion or another upload cannot race
-	// performs the same ownership check under its transaction.
+	// this final decision. The database unique index is a second line of defence.
-	current, err := uc.tasks.Get(ctx, in.TaskID)
+	var durable *domain.Artifact
+	err = uc.tx.WithinTx(ctx, func(ctx context.Context) error {
+		current, err := uc.tasks.GetForUpdate(ctx, in.TaskID)
+		if err != nil {
+			return err
+		}
+		if !current.IsLeaseHeldBy(in.WorkerID, in.Attempt, uc.clk.Now()) {
+			return domain.ErrLeaseConflict
+		}
+		existing, err := uc.artifacts.FindPartialResult(ctx, in.TaskID, in.Attempt)
+		if err != nil {
+			return err
+		}
+		if existing != nil {
+			durable = existing
+			return nil
+		}
+		if err := uc.artifacts.Insert(ctx, art); err != nil {
+			return err
+		}
+		durable = art
+		return nil
+	})
 	if err != nil {
 		_ = uc.blobs.Delete(ctx, art.StorageKey)
 		return nil, err
 	}
-	if !current.IsLeaseHeldBy(in.WorkerID, in.Attempt, uc.clk.Now()) {
+	if durable != art {
+		// Another request won the race while this stream was being written.
 		_ = uc.blobs.Delete(ctx, art.StorageKey)
-		return nil, domain.ErrLeaseConflict
 	}
-
+	return durable, nil
-	// Persist the record. If that fails the blob would be an orphan, so remove it.
-	if err := uc.artifacts.Insert(ctx, art); err != nil {
-		_ = uc.blobs.Delete(ctx, art.StorageKey)
-		return nil, err
-	}
-	return art, nil
 }
 
 // DownloadArtifact returns an artifact's metadata together with a reader over

coordinator/internal/usecase/job.go

@@ -33,6 +33,17 @@ func NewCreateJob(jobs JobRepository, tasks TaskRepository, tx TxManager, clock
 // The all-or-none guarantee comes from TxManager: a half-created job would
 // leave chunks no worker could ever complete.
 func (uc *CreateJob) Execute(ctx context.Context, in CreateJobInput) (*domain.Job, error) {
+	if in.Workload == "similarity-graph" || in.Workload == "similarity_graph" {
+		// CTX-10 must plan triangular block pairs; ordinary independent input
+		// chunks would silently omit every cross-chunk molecular pair.
+		return nil, domain.ErrInvalidInput
+	}
+	if (in.Workload == "similarity-search" || in.Workload == "similarity_search") &&
+		len(in.Chunks) > 1 && in.Parameters["query_id"] != nil {
+		// Resolving once against the source dataset belongs to CTX-07. Letting
+		// each shard resolve it would make most tasks fail or use inconsistent data.
+		return nil, domain.ErrInvalidInput
+	}
 	chunks := make([]domain.ChunkSpec, 0, len(in.Chunks))
 	for _, c := range in.Chunks {
 		chunks = append(chunks, domain.ChunkSpec(c))
@@ -92,6 +103,17 @@ func (uc *CancelJob) Execute(ctx context.Context, jobID uuid.UUID) (int64, error
 		if job.Status == domain.JobCompleted || job.Status == domain.JobFailed {
 			return domain.ErrJobNotCancellable
 		}
+		// The lease reaper can be the transition that exhausted the final task.
+		// Check the authoritative task histogram as well as the cached job status,
+		// so a stale status can never turn a failed/completed job into cancelled.
+		counts, err := uc.tasks.CountByStatus(ctx, jobID)
+		if err != nil {
+			return err
+		}
+		derived := progressFrom(*job, counts).DeriveStatus()
+		if derived == domain.JobCompleted || derived == domain.JobFailed {
+			return domain.ErrJobNotCancellable
+		}
 		cancelled, err = uc.tasks.CancelByJob(ctx, jobID, now)
 		if err != nil {
 			return err
@@ -212,3 +234,18 @@ func syncJobStatus(ctx context.Context, jobs JobRepository, tasks TaskRepository
 	}
 	return jobs.UpdateStatus(ctx, jobID, status, completedAt)
 }
+
+func syncExpiredJobStatuses(ctx context.Context, jobs JobRepository, tasks TaskRepository,
+	jobIDs []uuid.UUID, now time.Time) error {
+	seen := make(map[uuid.UUID]struct{}, len(jobIDs))
+	for _, jobID := range jobIDs {
+		if _, duplicate := seen[jobID]; duplicate {
+			continue
+		}
+		seen[jobID] = struct{}{}
+		if err := syncJobStatus(ctx, jobs, tasks, jobID, now); err != nil {
+			return err
+		}
+	}
+	return nil
+}

coordinator/internal/usecase/ports.go

@@ -60,9 +60,9 @@ type TaskRepository interface {
 	// lease. It returns how many tasks changed.
 	CancelByJob(ctx context.Context, jobID uuid.UUID, now time.Time) (int64, error)
 
-	// ExpireLeases applies the lease-expiry rule to every elapsed task and
+	// ExpireLeases applies the lease-expiry rule to every elapsed task and returns
-	// reports how many were affected.
+	// the distinct jobs whose aggregate status may have changed.
-	ExpireLeases(ctx context.Context, now time.Time) (int64, error)
+	ExpireLeases(ctx context.Context, now time.Time) ([]uuid.UUID, error)
 }
 
 // JobRepository persists jobs.
@@ -89,6 +89,9 @@ type WorkerRepository interface {
 type ArtifactRepository interface {
 	Insert(ctx context.Context, a *domain.Artifact) error
 	Get(ctx context.Context, id uuid.UUID) (*domain.Artifact, error)
+	// FindPartialResult returns the durable result already uploaded for one task
+	// attempt. A nil artifact means the attempt has not uploaded one yet.
+	FindPartialResult(ctx context.Context, taskID uuid.UUID, attempt int) (*domain.Artifact, error)
 }
 
 // BlobStore holds artifact bytes, addressed by an opaque storage key. It streams

coordinator/internal/usecase/task.go

@@ -21,12 +21,15 @@ import (
 
 type ClaimTask struct {
 	tasks         TaskRepository
+	jobs          JobRepository
+	workers       WorkerRepository
+	tx            TxManager
 	clock         Clock
 	leaseDuration time.Duration
 }
 
-func NewClaimTask(tasks TaskRepository, clock Clock, leaseDuration time.Duration) *ClaimTask {
+func NewClaimTask(tasks TaskRepository, jobs JobRepository, workers WorkerRepository, tx TxManager, clock Clock, leaseDuration time.Duration) *ClaimTask {
-	return &ClaimTask{tasks: tasks, clock: clock, leaseDuration: leaseDuration}
+	return &ClaimTask{tasks: tasks, jobs: jobs, workers: workers, tx: tx, clock: clock, leaseDuration: leaseDuration}
 }
 
 // Execute reclaims elapsed leases first, then hands out one task.
@@ -42,27 +45,46 @@ func (uc *ClaimTask) Execute(ctx context.Context, in ClaimTaskInput) (*domain.Cl
 	if in.WorkerID == "" {
 		return nil, domain.ErrInvalidInput
 	}
-	now := uc.clock.Now()
+	workloads := in.Workloads
-
+	if workerID, err := uuid.Parse(in.WorkerID); err == nil {
-	if _, err := uc.tasks.ExpireLeases(ctx, now); err != nil {
+		worker, err := uc.workers.Get(ctx, workerID)
-		return nil, err
+		if err != nil {
+			return nil, err
+		}
+		// Never trust caller-supplied capabilities: registration is the durable
+		// worker identity and its allowlist.
+		workloads = worker.Capabilities
 	}
+	var claimed *domain.ClaimedTask
+	err := uc.tx.WithinTx(ctx, func(ctx context.Context) error {
+		now := uc.clock.Now()
+		affectedJobs, err := uc.tasks.ExpireLeases(ctx, now)
+		if err != nil {
+			return err
+		}
+		if err := syncExpiredJobStatuses(ctx, uc.jobs, uc.tasks, affectedJobs, now); err != nil {
+			return err
+		}
 
-	task, err := uc.tasks.ClaimNext(ctx, ClaimFilter{
+		task, err := uc.tasks.ClaimNext(ctx, ClaimFilter{
-		Workloads:  in.Workloads,
+			Workloads:  workloads,
-		Owner:      in.WorkerID,
+			Owner:      in.WorkerID,
-		Now:        now,
+			Now:        now,
-		LeaseUntil: now.Add(uc.leaseDuration),
+			LeaseUntil: now.Add(uc.leaseDuration),
+		})
+		if err != nil {
+			return err
+		}
+		if task != nil {
+			value := task.AsClaimed()
+			claimed = &value
+		}
+		return nil
 	})
 	if err != nil {
 		return nil, err
 	}
-	if task == nil {
+	return claimed, nil // nil means an empty queue
-		return nil, nil // empty queue is a normal state, not an error
-	}
-
-	claimed := task.AsClaimed()
-	return &claimed, nil
 }
 
 // --- RenewLease ----------------------------------------------------------
@@ -230,18 +252,30 @@ func (uc *FailTask) Execute(ctx context.Context, in FailTaskInput) (*domain.Task
 
 type ExpireLeases struct {
 	tasks TaskRepository
+	jobs  JobRepository
+	tx    TxManager
 	clock Clock
 }
 
-func NewExpireLeases(tasks TaskRepository, clock Clock) *ExpireLeases {
+func NewExpireLeases(tasks TaskRepository, jobs JobRepository, tx TxManager, clock Clock) *ExpireLeases {
-	return &ExpireLeases{tasks: tasks, clock: clock}
+	return &ExpireLeases{tasks: tasks, jobs: jobs, tx: tx, clock: clock}
 }
 
-// Execute reports how many tasks were reclaimed.
+// Execute reclaims elapsed tasks and persists the state of every affected job.
 //
 // The sweep is one set-based statement rather than a load-decide-save loop:
 // several coordinators run it concurrently, and a single atomic UPDATE makes
 // the duplicate work harmless — the loser simply updates 0 rows.
 func (uc *ExpireLeases) Execute(ctx context.Context) (int64, error) {
-	return uc.tasks.ExpireLeases(ctx, uc.clock.Now())
+	var affected []uuid.UUID
+	err := uc.tx.WithinTx(ctx, func(ctx context.Context) error {
+		now := uc.clock.Now()
+		var err error
+		affected, err = uc.tasks.ExpireLeases(ctx, now)
+		if err != nil {
+			return err
+		}
+		return syncExpiredJobStatuses(ctx, uc.jobs, uc.tasks, affected, now)
+	})
+	return int64(len(affected)), err
 }

coordinator/internal/usecase/ui.go

@@ -15,6 +15,7 @@ type UIReadRepository interface {
 	GetJob(ctx context.Context, jobID uuid.UUID) (*domain.Job, error)
 	ListJobs(ctx context.Context, limit int) ([]domain.Job, error)
 	ListTasksByJob(ctx context.Context, jobID uuid.UUID) ([]domain.Task, error)
+	ListTasksByJobs(ctx context.Context, jobIDs []uuid.UUID) (map[uuid.UUID][]domain.Task, error)
 	ListWorkers(ctx context.Context, limit int) ([]domain.Worker, error)
 	ListArtifactsByJob(ctx context.Context, jobID uuid.UUID) ([]domain.Artifact, error)
 }
@@ -88,12 +89,16 @@ func (d *Dashboard) Overview(ctx context.Context, limit int) (DashboardView, err
 		return DashboardView{}, err
 	}
 	out := DashboardView{Jobs: make([]JobCard, 0, len(jobs)), Workers: make([]WorkerCard, 0, len(workers))}
+	jobIDs := make([]uuid.UUID, 0, len(jobs))
 	for _, job := range jobs {
-		tasks, err := d.read.ListTasksByJob(ctx, job.ID)
+		jobIDs = append(jobIDs, job.ID)
-		if err != nil {
+	}
-			return DashboardView{}, err
+	tasksByJob, err := d.read.ListTasksByJobs(ctx, jobIDs)
-		}
+	if err != nil {
-		out.Jobs = append(out.Jobs, jobCard(job, tasks))
+		return DashboardView{}, err
+	}
+	for _, job := range jobs {
+		out.Jobs = append(out.Jobs, jobCard(job, tasksByJob[job.ID]))
 	}
 	for _, worker := range workers {
 		out.Workers = append(out.Workers, WorkerCard{ID: worker.ID.String(), Name: worker.Name, Status: string(worker.Status), Capabilities: worker.Capabilities, LastHeartbeatAt: worker.LastHeartbeatAt})

coordinator/internal/usecase/upload.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"fmt"
 	"io"
+	"math"
 
 	"github.com/google/uuid"
 
@@ -15,20 +16,27 @@ import (
 // creates the job with one task per shard — the coordinator-side counterpart of
 // a client submitting pre-chunked URIs.
 type SubmitDataset struct {
-	blobs     BlobStore
+	blobs       BlobStore
-	artifacts ArtifactRepository
+	artifacts   ArtifactRepository
-	jobs      JobRepository
+	jobs        JobRepository
-	tasks     TaskRepository
+	tasks       TaskRepository
-	tx        TxManager
+	tx          TxManager
-	clk       Clock
+	clk         Clock
+	maxAttempts int
 }
 
 func NewSubmitDataset(blobs BlobStore, artifacts ArtifactRepository, jobs JobRepository,
-	tasks TaskRepository, tx TxManager, clk Clock) *SubmitDataset {
+	tasks TaskRepository, tx TxManager, clk Clock, maxAttempts int) *SubmitDataset {
-	return &SubmitDataset{blobs: blobs, artifacts: artifacts, jobs: jobs, tasks: tasks, tx: tx, clk: clk}
+	return &SubmitDataset{blobs: blobs, artifacts: artifacts, jobs: jobs, tasks: tasks, tx: tx, clk: clk, maxAttempts: maxAttempts}
 }
 
 func (uc *SubmitDataset) Execute(ctx context.Context, in SubmitDatasetInput) (SubmitDatasetResult, error) {
+	if err := validateUploadedWorkload(in.Workload, in.Parameters); err != nil {
+		return SubmitDatasetResult{}, err
+	}
+	if uc.maxAttempts < 1 {
+		return SubmitDatasetResult{}, domain.ErrInvalidInput
+	}
 	now := uc.clk.Now()
 
 	job, err := domain.NewUploadedJob(in.Workload, in.Parameters, now)
@@ -64,7 +72,7 @@ func (uc *SubmitDataset) Execute(ctx context.Context, in SubmitDatasetInput) (Su
 		cleanup()
 		return SubmitDatasetResult{}, err
 	}
-	splitErr := chunk.SplitTSVLimit(rc, in.RowsPerShard, in.MaxRows, func(index int, shard io.Reader) error {
+	splitErr := chunk.SplitChEMBLTSVLimit(rc, in.RowsPerShard, in.MaxRows, func(index int, shard io.Reader) error {
 		art, err := domain.NewArtifact(job.ID, nil, domain.ArtifactShard,
 			fmt.Sprintf("shard-%d.tsv", index), in.ContentType, now)
 		if err != nil {
@@ -77,7 +85,7 @@ func (uc *SubmitDataset) Execute(ctx context.Context, in SubmitDatasetInput) (Su
 		putKeys = append(putKeys, art.StorageKey)
 		art.SetContent(ssum, ssize)
 
-		task, err := domain.NewShardTask(job.ID, index, in.Workload, art.ID, ssum, in.Parameters, 0, now)
+		task, err := domain.NewShardTask(job.ID, index, in.Workload, art.ID, ssum, in.Parameters, uc.maxAttempts, now)
 		if err != nil {
 			return err
 		}
@@ -88,7 +96,8 @@ func (uc *SubmitDataset) Execute(ctx context.Context, in SubmitDatasetInput) (Su
 	_ = rc.Close()
 	if splitErr != nil {
 		cleanup()
-		return SubmitDatasetResult{}, splitErr
+		// Dataset shape is caller input, not an internal coordinator failure.
+		return SubmitDatasetResult{}, domain.ErrInvalidInput
 	}
 
 	// 3. Persist job + all artifacts + all tasks atomically.
@@ -118,6 +127,76 @@ func (uc *SubmitDataset) Execute(ctx context.Context, in SubmitDatasetInput) (Su
 	}, nil
 }
 
+// validateUploadedWorkload is deliberately narrow until CTX-07/08/10 adds a
+// typed distributed-workload registry. In particular, running similarity-graph
+// independently per TSV shard is scientifically wrong: cross-shard pairs would
+// be absent from the apparent graph.
+func validateUploadedWorkload(workload string, parameters map[string]any) error {
+	if workload != "similarity-search" {
+		return domain.ErrInvalidInput
+	}
+	allowed := map[string]struct{}{
+		"query_smiles": {}, "top_k": {}, "threshold": {},
+		"threshold_direction": {}, "progress_every": {},
+	}
+	for key := range parameters {
+		if _, ok := allowed[key]; !ok {
+			return domain.ErrInvalidInput
+		}
+	}
+	query, ok := parameters["query_smiles"].(string)
+	if !ok || query == "" || len(query) > 200 {
+		return domain.ErrInvalidInput
+	}
+	if value, ok := parameters["top_k"]; ok && !isPositiveJSONInteger(value) {
+		return domain.ErrInvalidInput
+	}
+	if value, ok := parameters["progress_every"]; ok && !isNonNegativeJSONInteger(value) {
+		return domain.ErrInvalidInput
+	}
+	if value, ok := parameters["threshold"]; ok && !isUnitIntervalNumber(value) {
+		return domain.ErrInvalidInput
+	}
+	if value, ok := parameters["threshold_direction"]; ok && value != "greater" && value != "less" {
+		return domain.ErrInvalidInput
+	}
+	return nil
+}
+
+func isPositiveJSONInteger(value any) bool    { return isJSONInteger(value, false) }
+func isNonNegativeJSONInteger(value any) bool { return isJSONInteger(value, true) }
+
+func isJSONInteger(value any, allowZero bool) bool {
+	var n int64
+	switch v := value.(type) {
+	case int:
+		n = int64(v)
+	case int64:
+		n = v
+	case float64:
+		if math.Trunc(v) != v || v > math.MaxInt64 || v < math.MinInt64 {
+			return false
+		}
+		n = int64(v)
+	default:
+		return false
+	}
+	return n >= 0 && (allowZero || n > 0)
+}
+
+func isUnitIntervalNumber(value any) bool {
+	switch v := value.(type) {
+	case float64:
+		return !math.IsNaN(v) && !math.IsInf(v, 0) && v >= 0 && v <= 1
+	case int:
+		return v >= 0 && v <= 1
+	case int64:
+		return v >= 0 && v <= 1
+	default:
+		return false
+	}
+}
+
 // GetTaskInput resolves a task's input shard and opens it for streaming. The
 // caller closes the reader.
 type GetTaskInput struct {

coordinator/internal/usecase/usecase_test.go

@@ -68,18 +68,18 @@ func newHarness() *harness {
 	}
 	tx := memstore.Tx{}
 	h.createJob = usecase.NewCreateJob(h.jobs, h.tasks, tx, h.clk)
-	h.submit = usecase.NewSubmitDataset(h.blobs, h.arts, h.jobs, h.tasks, tx, h.clk)
+	h.submit = usecase.NewSubmitDataset(h.blobs, h.arts, h.jobs, h.tasks, tx, h.clk, 3)
-	h.claim = usecase.NewClaimTask(h.tasks, h.clk, lease)
+	h.claim = usecase.NewClaimTask(h.tasks, h.jobs, h.work, tx, h.clk, lease)
 	h.renew = usecase.NewRenewLease(h.tasks, h.work, tx, h.clk, lease)
 	h.complete = usecase.NewCompleteTask(h.tasks, h.jobs, h.arts, tx, h.clk)
 	h.fail = usecase.NewFailTask(h.tasks, h.jobs, tx, h.clk)
 	h.status = usecase.NewGetJobStatus(h.jobs, h.tasks)
 	h.results = usecase.NewListResults(h.tasks)
 	h.register = usecase.NewRegisterWorker(h.work, h.clk)
-	h.uploadArt = usecase.NewUploadArtifact(h.tasks, h.arts, h.blobs, h.clk)
+	h.uploadArt = usecase.NewUploadArtifact(h.tasks, h.arts, h.blobs, tx, h.clk)
 	h.downloadArt = usecase.NewDownloadArtifact(h.arts, h.blobs)
 	h.getInput = usecase.NewGetTaskInput(h.tasks, h.arts, h.blobs)
-	h.expire = usecase.NewExpireLeases(h.tasks, h.clk)
+	h.expire = usecase.NewExpireLeases(h.tasks, h.jobs, tx, h.clk)
 	h.cancel = usecase.NewCancelJob(h.jobs, h.tasks, tx, h.clk)
 	return h
 }
@@ -138,6 +138,44 @@ func TestClaimLeasesAndAdvancesAttempt(t *testing.T) {
 	}
 }
 
+func TestRegisteredWorkerCannotBroadenItsCapabilitiesAtClaim(t *testing.T) {
+	h := newHarness()
+	h.seedJob(t, "restricted", 1)
+	worker, err := h.register.Execute(ctx, usecase.RegisterWorkerInput{
+		Name: "search-only", Capabilities: []string{"similarity-search"},
+	})
+	if err != nil {
+		t.Fatal(err)
+	}
+	claimed, err := h.claim.Execute(ctx, usecase.ClaimTaskInput{
+		WorkerID: worker.ID.String(), Workloads: []string{"restricted"},
+	})
+	if err != nil || claimed != nil {
+		t.Fatalf("claim = (%v, %v), want no compatible task", claimed, err)
+	}
+}
+
+func TestCreateJobRejectsUnsafeDistributedScientificPlans(t *testing.T) {
+	h := newHarness()
+	_, err := h.createJob.Execute(ctx, usecase.CreateJobInput{
+		Workload: "similarity-graph", InputURI: "s3://input",
+		Chunks: []usecase.ChunkInput{{ChunkIndex: 0, InputURI: "s3://chunk", InputSHA256: "sha"}},
+	})
+	if !errors.Is(err, domain.ErrInvalidInput) {
+		t.Errorf("graph job err = %v, want ErrInvalidInput", err)
+	}
+	_, err = h.createJob.Execute(ctx, usecase.CreateJobInput{
+		Workload: "similarity-search", InputURI: "s3://input", Parameters: map[string]any{"query_id": "CHEMBL1"},
+		Chunks: []usecase.ChunkInput{
+			{ChunkIndex: 0, InputURI: "s3://chunk0", InputSHA256: "sha"},
+			{ChunkIndex: 1, InputURI: "s3://chunk1", InputSHA256: "sha"},
+		},
+	})
+	if !errors.Is(err, domain.ErrInvalidInput) {
+		t.Errorf("sharded query_id job err = %v, want ErrInvalidInput", err)
+	}
+}
+
 func TestClaimEmptyQueueReturnsNil(t *testing.T) {
 	h := newHarness()
 	c, err := h.claim.Execute(ctx, usecase.ClaimTaskInput{WorkerID: "w1", Workloads: []string{"w"}})
@@ -281,7 +319,7 @@ func TestUploadRejectsLeaseThatExpiresDuringStreaming(t *testing.T) {
 	h.seedJob(t, "w", 1)
 	taskID, attempt := h.leaseOne(t, "w1", "w")
 	h.uploadArt = usecase.NewUploadArtifact(
-		h.tasks, h.arts, expiringBlobStore{BlobStore: h.blobs, clock: h.clk}, h.clk,
+		h.tasks, h.arts, expiringBlobStore{BlobStore: h.blobs, clock: h.clk}, memstore.Tx{}, h.clk,
 	)
 
 	_, err := h.uploadArt.Execute(ctx, usecase.UploadArtifactInput{
@@ -414,6 +452,23 @@ func TestUploadArtifactRejectsForeignWorker(t *testing.T) {
 	}
 }
 
+func TestUploadArtifactIsIdempotentPerTaskAttempt(t *testing.T) {
+	h := newHarness()
+	h.seedJob(t, "w", 1)
+	taskID, attempt := h.leaseOne(t, "w1", "w")
+	first := h.uploadResult(t, taskID, "w1", attempt)
+	second, err := h.uploadArt.Execute(ctx, usecase.UploadArtifactInput{
+		TaskID: taskID, WorkerID: "w1", Attempt: attempt,
+		Filename: "retry.csv", ContentType: "text/csv", Body: strings.NewReader("different bytes"),
+	})
+	if err != nil {
+		t.Fatal(err)
+	}
+	if second.ID != first {
+		t.Errorf("retry artifact = %s, want existing %s", second.ID, first)
+	}
+}
+
 func TestDownloadArtifactRoundTrips(t *testing.T) {
 	h := newHarness()
 	h.seedJob(t, "w", 1)
@@ -434,10 +489,10 @@ func TestDownloadArtifactRoundTrips(t *testing.T) {
 
 func TestSubmitDatasetChunksAndServesInput(t *testing.T) {
 	h := newHarness()
-	tsv := "id\tsmiles\nA\tCC\nB\tCCC\nC\tCCCC\nD\tCCCCC\nE\tCCCCCC\n"
+	tsv := "chembl_id\tcanonical_smiles\nA\tCC\nB\tCCC\nC\tCCCC\nD\tCCCCC\nE\tCCCCCC\n"
 
 	res, err := h.submit.Execute(ctx, usecase.SubmitDatasetInput{
-		Workload: "w", RowsPerShard: 2, Filename: "chembl.tsv",
+		Workload: "similarity-search", Parameters: map[string]any{"query_smiles": "CCO"}, RowsPerShard: 2, Filename: "chembl.tsv",
 		ContentType: "text/tab-separated-values", Body: strings.NewReader(tsv),
 	})
 	if err != nil {
@@ -453,7 +508,7 @@ func TestSubmitDatasetChunksAndServesInput(t *testing.T) {
 		t.Errorf("job total = %d, want 3", prog.Total)
 	}
 
-	c, err := h.claim.Execute(ctx, usecase.ClaimTaskInput{WorkerID: "w1", Workloads: []string{"w"}})
+	c, err := h.claim.Execute(ctx, usecase.ClaimTaskInput{WorkerID: "w1", Workloads: []string{"similarity-search"}})
 	if err != nil || c == nil {
 		t.Fatalf("claim shard: %v", err)
 	}
@@ -472,9 +527,9 @@ func TestSubmitDatasetChunksAndServesInput(t *testing.T) {
 
 func TestSubmitDatasetLimitsRowsBeforeCreatingShards(t *testing.T) {
 	h := newHarness()
-	tsv := "id\tsmiles\nA\tCC\nB\tCCC\nC\tCCCC\nD\tCCCCC\nE\tCCCCCC\n"
+	tsv := "chembl_id\tcanonical_smiles\nA\tCC\nB\tCCC\nC\tCCCC\nD\tCCCCC\nE\tCCCCCC\n"
 	res, err := h.submit.Execute(ctx, usecase.SubmitDatasetInput{
-		Workload: "w", RowsPerShard: 2, MaxRows: 3, Filename: "chembl.tsv",
+		Workload: "similarity-search", Parameters: map[string]any{"query_smiles": "CCO"}, RowsPerShard: 2, MaxRows: 3, Filename: "chembl.tsv",
 		ContentType: "text/tab-separated-values", Body: strings.NewReader(tsv),
 	})
 	if err != nil {
@@ -485,6 +540,26 @@ func TestSubmitDatasetLimitsRowsBeforeCreatingShards(t *testing.T) {
 	}
 }
 
+func TestSubmitDatasetRejectsUnsupportedDistributedWorkloads(t *testing.T) {
+	h := newHarness()
+	_, err := h.submit.Execute(ctx, usecase.SubmitDatasetInput{
+		Workload: "similarity-graph", Parameters: map[string]any{"threshold": 0.7}, RowsPerShard: 2,
+		Filename: "chembl.tsv", ContentType: "text/tab-separated-values",
+		Body: strings.NewReader("chembl_id\tcanonical_smiles\nA\tCC\n"),
+	})
+	if !errors.Is(err, domain.ErrInvalidInput) {
+		t.Errorf("graph submission err = %v, want ErrInvalidInput", err)
+	}
+	_, err = h.submit.Execute(ctx, usecase.SubmitDatasetInput{
+		Workload: "similarity-search", Parameters: map[string]any{"query_id": "CHEMBL1"}, RowsPerShard: 2,
+		Filename: "chembl.tsv", ContentType: "text/tab-separated-values",
+		Body: strings.NewReader("chembl_id\tcanonical_smiles\nA\tCC\n"),
+	})
+	if !errors.Is(err, domain.ErrInvalidInput) {
+		t.Errorf("query_id submission err = %v, want ErrInvalidInput", err)
+	}
+}
+
 func TestCancelJobInvalidatesClaimedAndPendingTasks(t *testing.T) {
 	h := newHarness()
 	jobID := h.seedJob(t, "w", 3)
@@ -531,3 +606,22 @@ func TestExpireLeasesReclaims(t *testing.T) {
 		t.Errorf("expire = (%d, %v), want (1, nil)", n, err)
 	}
 }
+
+func TestFinalLeaseExpiryPersistsFailedJobAndCannotBeCancelled(t *testing.T) {
+	h := newHarness()
+	jobID := h.seedJob(t, "w", 1)
+	for attempt := 1; attempt <= domain.DefaultMaxAttempts; attempt++ {
+		h.leaseOne(t, "w1", "w")
+		h.clk.Advance(lease + time.Second)
+		if _, err := h.expire.Execute(ctx); err != nil {
+			t.Fatalf("expire attempt %d: %v", attempt, err)
+		}
+	}
+	progress, err := h.status.Execute(ctx, jobID)
+	if err != nil || progress.Job.Status != domain.JobFailed || progress.DeriveStatus() != domain.JobFailed {
+		t.Fatalf("progress = %+v, err = %v; want persisted failed job", progress, err)
+	}
+	if _, err := h.cancel.Execute(ctx, jobID); !errors.Is(err, domain.ErrJobNotCancellable) {
+		t.Errorf("cancel terminal lease failure = %v, want ErrJobNotCancellable", err)
+	}
+}

coordinator/migrations/0009_unique_partial_result_attempt.down.sql

@@ -0,0 +1,5 @@
+BEGIN;
+
+DROP INDEX IF EXISTS uq_partial_result_task_attempt;
+
+COMMIT;

coordinator/migrations/0009_unique_partial_result_attempt.up.sql

@@ -0,0 +1,26 @@
+BEGIN;
+
+-- Old deployments can contain more than one partial result because earlier
+-- versions accepted repeated PUTs. Preserve the one referenced by a completed
+-- task and discard stale rows; unfinished tasks must upload again after a
+-- deploy, just as they do after a lost lease.
+DELETE FROM artifacts AS a
+USING tasks AS t
+WHERE a.task_id = t.id
+  AND a.kind = 'partial_result'::artifact_kind
+  AND t.status <> 'completed'::task_status;
+
+DELETE FROM artifacts AS a
+USING tasks AS t
+WHERE a.task_id = t.id
+  AND a.kind = 'partial_result'::artifact_kind
+  AND t.status = 'completed'::task_status
+  AND a.id <> t.result_artifact_id;
+
+-- One lease attempt has one durable partial result. This makes an upload retry
+-- idempotent and prevents repeated uploads from accumulating orphan artifacts.
+CREATE UNIQUE INDEX uq_partial_result_task_attempt
+    ON artifacts (task_id, attempt)
+    WHERE kind = 'partial_result'::artifact_kind;
+
+COMMIT;

coordinator/scripts/smoke.sh

@@ -51,6 +51,13 @@ check "register worker"                 201 -X POST "${HOST}/workers/register" "
 	-d '{"name":"smoke-worker","capabilities":["similarity_search"],"cpu_count":4,"memory_mb":8192}'
 check "register without capabilities → 400" 400 -X POST "${HOST}/workers/register" "${auth[@]}" \
 	-d '{"name":"bad"}'
+registration=$(curl -sS "${auth[@]}" -X POST "${HOST}/workers/register" \
+	-d '{"name":"smoke-worker-active","capabilities":["similarity_search","similarity-search"],"cpu_count":4}')
+worker_id=$(printf '%s' "$registration" | python3 -c 'import json,sys;print(json.load(sys.stdin)["worker_id"])' 2>/dev/null)
+if [[ -z "${worker_id:-}" ]]; then
+	echo "  ✗ could not register active worker: $registration"
+	exit 1
+fi
 
 echo
 echo "job lifecycle"
@@ -75,7 +82,7 @@ declare -A our_chunks
 task_id=""
 attempt=""
 for _ in $(seq 1 40); do
-	claim=$(curl -sS "${auth[@]}" -X POST "${HOST}/tasks/claim" -d '{"worker_id":"w1"}')
+	claim=$(curl -sS "${auth[@]}" -X POST "${HOST}/tasks/claim" -d "{\"worker_id\":\"${worker_id}\"}")
 	[[ -z "$claim" ]] && break # 204: queue drained
 
 	read -r c_job c_task c_chunk c_attempt < <(printf '%s' "$claim" |
@@ -100,7 +107,7 @@ else
 fi
 
 check "heartbeat"                          200 -X POST "${HOST}/tasks/${task_id}/heartbeat" "${auth[@]}" \
-	-d "{\"worker_id\":\"w1\",\"attempt\":${attempt}}"
+	-d "{\"worker_id\":\"${worker_id}\",\"attempt\":${attempt}}"
 
 # --- artifacts + result (uploads happen while the task is still leased) ---
 bearer=(-H "Authorization: Bearer ${TOKEN}")
@@ -108,43 +115,47 @@ bearer=(-H "Authorization: Bearer ${TOKEN}")
 # upload <filename> -> prints the artifact_id
 upload() {
 	curl -sS -X PUT "${HOST}/tasks/${task_id}/artifacts/$1" "${bearer[@]}" \
-		-H 'Content-Type: text/csv' -H 'X-Worker-ID: w1' -H "X-Task-Attempt: ${attempt}" \
+		-H 'Content-Type: text/csv' -H "X-Worker-ID: ${worker_id}" -H "X-Task-Attempt: ${attempt}" \
 		--data-binary $'query,match,score\nA,B,0.9\n' |
 		python3 -c 'import json,sys;print(json.load(sys.stdin)["artifact_id"])' 2>/dev/null
 }
 
 check "upload artifact"                    200 -X PUT "${HOST}/tasks/${task_id}/artifacts/result.csv" "${bearer[@]}" \
-	-H 'Content-Type: text/csv' -H 'X-Worker-ID: w1' -H "X-Task-Attempt: ${attempt}" \
+	-H 'Content-Type: text/csv' -H "X-Worker-ID: ${worker_id}" -H "X-Task-Attempt: ${attempt}" \
 	--data-binary $'query,match,score\nA,B,0.9\n'
 check "foreign worker upload → 409"        409 -X PUT "${HOST}/tasks/${task_id}/artifacts/x.csv" "${bearer[@]}" \
 	-H 'Content-Type: text/csv' -H 'X-Worker-ID: impostor' -H "X-Task-Attempt: ${attempt}" \
 	--data-binary 'x'
 
-# Two result artifacts, uploaded now while the lease is held: one to complete
+# A retry of a PUT returns the same durable artifact for the task attempt.
-# with, a second to prove a different manifest is rejected after completion.
 art_id=$(upload primary.csv)
 art_id2=$(upload secondary.csv)
+if [[ "$art_id" == "$art_id2" ]]; then
+	printf '  \033[32m✓\033[0m %-46s %s\n' "duplicate upload is idempotent" "$art_id"
+	pass=$((pass + 1))
+else
+	printf '  \033[31m✗\033[0m %-46s got %s and %s\n' "duplicate upload is idempotent" "$art_id" "$art_id2"
+	fail=$((fail + 1))
+fi
 check "download artifact"                  200 "${HOST}/artifacts/${art_id}/download" "${bearer[@]}"
 
 check "foreign worker submits → 409"       409 -X POST "${HOST}/tasks/${task_id}/result" "${auth[@]}" \
 	-d "{\"worker_id\":\"impostor\",\"attempt\":${attempt},\"result\":{\"artifact_id\":\"${art_id}\"}}"
 check "submit result"                      200 -X POST "${HOST}/tasks/${task_id}/result" "${auth[@]}" \
-	-d "{\"worker_id\":\"w1\",\"attempt\":${attempt},\"result\":{\"artifact_id\":\"${art_id}\"}}"
+	-d "{\"worker_id\":\"${worker_id}\",\"attempt\":${attempt},\"result\":{\"artifact_id\":\"${art_id}\"}}"
 check "replay same result → idempotent"    200 -X POST "${HOST}/tasks/${task_id}/result" "${auth[@]}" \
-	-d "{\"worker_id\":\"w1\",\"attempt\":${attempt},\"result\":{\"artifact_id\":\"${art_id}\"}}"
+	-d "{\"worker_id\":\"${worker_id}\",\"attempt\":${attempt},\"result\":{\"artifact_id\":\"${art_id}\"}}"
-check "different result → 409"             409 -X POST "${HOST}/tasks/${task_id}/result" "${auth[@]}" \
-	-d "{\"worker_id\":\"w1\",\"attempt\":${attempt},\"result\":{\"artifact_id\":\"${art_id2}\"}}"
 check "GET /jobs/{id}"                     200 "${HOST}/jobs/${job_id}" "${auth[@]}"
 
 echo
 echo "input validation"
 check "malformed uuid → 400"               400 -X POST "${HOST}/tasks/not-a-uuid/result" "${auth[@]}" \
-	-d '{"worker_id":"w1","attempt":1,"result":{"artifact_id":"00000000-0000-0000-0000-000000000000"}}'
+	-d "{\"worker_id\":\"${worker_id}\",\"attempt\":1,\"result\":{\"artifact_id\":\"00000000-0000-0000-0000-000000000000\"}}"
 # Note: Go's encoding/json matches field names case-insensitively, so
 # "worker_ID" would be accepted as "worker_id". Only a genuinely unknown key
 # trips DisallowUnknownFields.
 check "unknown json field → 400"           400 -X POST "${HOST}/tasks/claim" "${auth[@]}" \
-	-d '{"worker_id":"w1","totally_unknown":1}'
+	-d "{\"worker_id\":\"${worker_id}\",\"totally_unknown\":1}"
 check "unknown job → 404"                  404 "${HOST}/jobs/00000000-0000-0000-0000-000000000000" "${auth[@]}"
 
 echo
@@ -152,11 +163,11 @@ echo "dataset upload → chunking"
 # Upload a 5-row TSV split at 2 rows/shard → expect 3 shard tasks. The text
 # fields precede the file part, which the coordinator streams.
 up=$(curl -sS "${bearer[@]}" -X POST "${HOST}/jobs/upload" \
-	-F 'workload=similarity_search' \
+	-F 'workload=similarity-search' \
-	-F 'parameters={"top_k":10}' \
+	-F 'parameters={"query_smiles":"CCO","top_k":10}' \
 	-F 'chunk_rows=2' \
 	-F 'file=@-;filename=chembl.tsv;type=text/tab-separated-values' <<'TSV'
-id	smiles
+chembl_id	canonical_smiles
 A	CC
 B	CCC
 C	CCCC
@@ -180,7 +191,7 @@ fi
 up_input=""
 for _ in $(seq 1 30); do
 	c=$(curl -sS "${bearer[@]}" -H 'Content-Type: application/json' -X POST "${HOST}/tasks/claim" \
-		-d '{"worker_id":"up-w","capabilities":["similarity_search"]}')
+		-d "{\"worker_id\":\"${worker_id}\"}")
 	[[ -z "$c" ]] && break
 	cj=$(printf '%s' "$c" | python3 -c 'import json,sys;print(json.load(sys.stdin)["job_id"])' 2>/dev/null)
 	[[ "$cj" != "$up_job" ]] && continue

docs/api-contract.md

@@ -107,7 +107,8 @@ Content-Type: application/json
 ```
 
 `cpu_count`/`memory_mb` are accepted for forward compatibility and not yet
-persisted. `capabilities` must be non-empty (an allowlisted workload set).
+persisted. `capabilities` must be non-empty. A claim uses the capabilities
+stored at registration; the request cannot broaden them.
 
 ## Claim task
 
@@ -120,7 +121,8 @@ Content-Type: application/json
 ```
 
 - `204 No Content`: no compatible task.
-- `200 OK`: a task is leased atomically.
+- `200 OK`: a task is leased atomically. `worker_id` must be a registered UUID;
+  its persisted capabilities, rather than this request field, decide eligibility.
 
 ```json
 {

docs/building-workers.md

@@ -46,24 +46,25 @@ coordinator was started with. Never log it, never send it in an error body.
 
 ```http
 POST /workers/register
-{ "name": "lab-worker-01", "capabilities": ["similarity_search"] }
+{ "name": "lab-worker-01", "capabilities": ["similarity-search"] }
 ```
 
 Response: `{ "worker_id": "<uuid>", "heartbeat_interval_seconds": 15 }`.
 
-- `capabilities` are the workload names you can run — the coordinator only hands
+- `capabilities` are fixed at registration — the coordinator only hands you
-  you matching tasks.
+  matching tasks and a later claim cannot broaden that set.
 - **Keep `worker_id`**. Use it as your identity in every later call. Using the
   registered UUID is what lets the coordinator track your liveness (it marks
   workers offline after they go silent).
-- Current coordinator jobs use `similarity_search` / `similarity_graph`; the
+- Current diagnostic uploads use `similarity-search` with `query_smiles`. The
-  reference Python worker also accepts the public CLI spellings with hyphens.
+  reference worker accepts the legacy `similarity_search` spelling too. Do not
+  advertise `similarity-graph` until CTX-10 implements cross-shard pair planning.
 
 ## 2. Claim a task
 
 ```http
 POST /tasks/claim
-{ "worker_id": "<uuid>", "capabilities": ["similarity_search"] }
+{ "worker_id": "<uuid>", "capabilities": ["similarity-search"] }
 ```
 
 - `200` → a leased task (below).
@@ -74,9 +75,9 @@ POST /tasks/claim
   "task_id": "<uuid>",
   "attempt": 1,
   "lease_expires_at": "2026-07-22T12:05:00Z",
-  "workload": "similarity_search",
+  "workload": "similarity-search",
   "input": { "uri": "/tasks/<uuid>/input", "sha256": "<hex>" },
-  "parameters": { "query_id": "CHEMBL939", "top_k": 20 }
+  "parameters": { "query_smiles": "CCO", "top_k": 20 }
 }
 ```
 
@@ -193,6 +194,32 @@ Per the worker contract, at minimum:
 - poll interval and request timeout
 - a working directory for downloaded inputs and generated outputs
 
+## Run the reference worker locally
+
+Use one terminal per worker and a distinct work directory for each process:
+
+```sh
+SCIMESH_COORDINATOR_URL=http://localhost:8080 \
+SCIMESH_BEARER_TOKEN=dev-token \
+SCIMESH_WORKER_NAME=worker-1 \
+scimesh-worker --work-dir "$PWD/worker-data-1"
+```
+
+For a bounded manual check, use one of these lifecycle modes:
+
+```sh
+# Make exactly one claim; exit immediately when no task is available.
+scimesh-worker --work-dir "$PWD/worker-data-check" --once
+
+# Keep polling until two tasks complete successfully, then exit.
+scimesh-worker --work-dir "$PWD/worker-data-check" --max-tasks 2
+```
+
+`SCIMESH_MAX_TASKS` provides the same limit through the environment. Pressing
+`Ctrl+C` stops the reference worker cleanly. If it interrupts an active task,
+the worker reports a sanitized retriable failure first, emits no traceback, and
+exits with status `130`.
+
 ## Generate a client from the spec
 
 Instead of hand-writing request code, generate it:

docs/ctx-07-distributed-workload-protocol.md

@@ -0,0 +1,207 @@
+# CTX-07: distributed workload protocol and planner contract
+
+## Status and scope
+
+This document is the implementation contract for CTX-07. It does not implement
+a planner, reducer, API endpoint, database migration, or final artifact. Until
+CTX-08 and CTX-09 are complete, shard CSVs remain diagnostic partial results.
+
+The protocol gives local scientific workloads a coordinator-independent way to
+validate a job, plan artifact-backed tasks, and later reduce completed outputs.
+The Go coordinator owns durable artifacts, transactions, task rows, leases, and
+HTTP. A Python workload must never access PostgreSQL or call the coordinator.
+
+Read `PLAN.md`, `.agents/workloads.md`, and `docs/api-contract.md` before
+implementing this CTX.
+
+## Canonical vocabulary
+
+- External workload names are lowercase hyphenated names: `similarity-search`
+  and, later, `similarity-graph`.
+- The existing underscore spellings are a temporary compatibility alias at the
+  Python worker boundary only. Planners, persisted job/task payloads, and new
+  API examples use the canonical hyphenated spelling.
+- A **plan** contains only JSON-compatible values and coordinator artifact
+  references. It contains no local filesystem path, worker URI, presigned URL,
+  database connection, or callable.
+- `chunk_index` is a non-negative integer, unique within a plan, and sorted
+  ascending whenever results are enumerated.
+
+## Python boundary
+
+CTX-07 adds a small `DistributedWorkload` protocol under `scimesh/distributed/`
+and a registry separate from the local CLI registry. Names below are proposed
+public types; keep concrete implementation details minimal.
+
+```python
+class DistributedWorkload(Protocol):
+    name: str
+
+    def validate_job(self, parameters: Mapping[str, object]) -> None: ...
+
+    def plan(
+        self,
+        input_path: Path,
+        input_artifact_id: str,
+        parameters: Mapping[str, object],
+        shard_rows: int,
+        workspace: Path,
+    ) -> DistributedPlan: ...
+
+    def reduce(
+        self,
+        partial_results: Sequence[CompletedPartial],
+        parameters: Mapping[str, object],
+        workspace: Path,
+    ) -> FinalResult: ...
+```
+
+`input_path` and `workspace` are temporary files supplied by the coordinator
+bridge. They are never serialized. `plan()` returns only a `DistributedPlan`;
+the bridge validates it, persists artifact/task rows in one coordinator
+transaction, and removes its temporary workspace. If validation or planning
+fails, no job or task may be written.
+
+## JSON models
+
+All objects below are schema version `1`. Future incompatible changes require a
+new version; never infer a schema from missing fields.
+
+### Artifact reference
+
+```json
+{
+  "artifact_id": "c4273293-f8b4-4ecb-99df-3b9f5a32b6a6",
+  "sha256": "3b2d...64-lowercase-hex-characters",
+  "content_type": "text/tab-separated-values"
+}
+```
+
+The artifact ID is coordinator-owned. The checksum is included so planning and
+tests can assert exactly which immutable input was used. A worker receives the
+coordinator-generated download URI only through `POST /tasks/claim`.
+
+### Distributed plan
+
+```json
+{
+  "schema_version": 1,
+  "workload": "similarity-search",
+  "resolved_parameters": {
+    "query_smiles": "COc1ccc(Nc2ncnc3cc(OCCCN4CCOCC4)c(OC)c23)cc1",
+    "query_source": {"kind": "chembl_id", "value": "CHEMBL939"},
+    "top_k": 20,
+    "threshold": 0.7,
+    "threshold_direction": "greater",
+    "fingerprint": {"algorithm": "morgan", "radius": 2, "fp_size": 2048}
+  },
+  "tasks": [
+    {
+      "chunk_index": 0,
+      "input_artifact": {
+        "artifact_id": "69e41105-d9fb-4c7f-a2db-7dd9e3ba2c76",
+        "sha256": "4c92...64-lowercase-hex-characters",
+        "content_type": "text/tab-separated-values"
+      },
+      "parameters": {
+        "query_smiles": "COc1ccc(Nc2ncnc3cc(OCCCN4CCOCC4)c(OC)c23)cc1",
+        "top_k": 20,
+        "threshold": 0.7,
+        "threshold_direction": "greater",
+        "fingerprint": {"algorithm": "morgan", "radius": 2, "fp_size": 2048}
+      }
+    }
+  ]
+}
+```
+
+`resolved_parameters` are immutable job metadata. A task copies only the
+values required by its worker runner. The coordinator may add its own durable
+task ID and generated input URI; it must not alter scientific parameters.
+
+## Similarity-search planning rules
+
+1. Accept exactly one of `query_id` and `query_smiles` at the public boundary.
+2. Validate a supplied SMILES once. For `query_id`, find and validate that
+   molecule once against the original uploaded TSV **before** creating shards.
+3. Persist the resolved canonical query SMILES and the original query source in
+   `resolved_parameters`. Workers receive `query_smiles`, never `query_id`.
+4. Fingerprint settings are fixed to Morgan radius `2` and `fp_size` `2048`.
+   Reject a request that tries to override them rather than silently changing
+   scientific semantics.
+5. Split source rows in input order. Every shard includes the original TSV
+   header and has a contiguous, zero-based `chunk_index`.
+6. Each shard uses the global `top_k`, not a smaller local limit. A global
+   reducer cannot recover a candidate discarded by every shard.
+7. Preserve `threshold`, `threshold_direction`, and valid `max_rows` semantics
+   in the resolved plan. A job-level row limit is applied before sharding, not
+   independently by every worker.
+
+Invalid row SMILES are not planner failures. They remain shard data and are
+counted by the worker exactly as the local workload does. An invalid query is a
+planning failure.
+
+## Partial-result contract
+
+A completed similarity-search task owns exactly one coordinator-uploaded CSV
+artifact with content type `text/csv` and these columns, in this order:
+
+```csv
+rank,chembl_id,canonical_smiles,similarity
+1,CHEMBL123,CCO,0.875000
+```
+
+- `rank` is one-based local rank.
+- `similarity` uses the local CLI's six-decimal formatting.
+- Rows are sorted by `(-similarity, chembl_id, canonical_smiles)` for
+  `threshold_direction=greater`, or `(similarity, chembl_id,
+  canonical_smiles)` for `less`.
+- The query molecule and every candidate with the same canonical query SMILES
+  are excluded using the existing local-workload definition.
+- Empty valid result files still include the header.
+
+The worker completion metrics must include JSON numbers for `scanned_rows`,
+`valid_molecules`, `invalid_smiles`, `matches_emitted`, and
+`elapsed_seconds`. Metrics are observability data; the reducer derives final
+scientific output exclusively from coordinator-owned partial artifacts.
+
+## Reduction boundary
+
+CTX-09 invokes the registered reducer only after every task is completed. It
+passes `CompletedPartial` values ordered by `chunk_index`, each containing its
+coordinator artifact reference and validated metrics.
+
+For similarity-search the reducer:
+
+1. reads partial CSVs in `chunk_index` order;
+2. validates header, row shape, rank, finite similarity in `[0, 1]`, and sort
+   order;
+3. retains a bounded heap of at most the global `top_k` candidates using the
+   exact local ranking key;
+4. writes the same header and deterministic rank numbering as the local CLI.
+
+It must not deduplicate ordinary records: the local reference keeps input-row
+multiplicity. Reduction is independent of worker completion order and uses
+`O(top_k + shard_rows)` memory apart from CSV streaming buffers.
+
+## Required tests for the CTX-07 implementation
+
+- unknown workload is rejected before any coordinator job/task write;
+- invalid public parameters and invalid `query_id` produce no partial plan;
+- `query_id` resolution occurs once, before shard construction;
+- the same input, parameters, and shard size generate byte-equivalent
+  JSON plans and identical shard order;
+- every task payload is JSON-serializable and contains only artifact references
+  and validated scalar/object values;
+- a two-shard dummy workload proves coordinator transaction rollback on planner
+  validation failure;
+- completed partial artifacts reach the reducer ordered by `chunk_index`, even
+  when workers finish in a different order;
+- the protocol registry never imports the Go coordinator or database code.
+
+## Deferred work
+
+CTX-08 implements the similarity-search planner, runner adapter, reducer, and
+comparison against the local CLI. CTX-09 persists the final artifact and job
+state. CTX-10 defines graph-specific triangular block plans; it must not reuse
+the search shard scheme without its pair-coverage invariants.

docs/openapi.yaml

@@ -96,7 +96,9 @@ paths:
       description: >
         multipart/form-data. The text fields (`workload`, `parameters`,
         `chunk_rows`, `max_rows`) MUST precede the `file` part: the file is streamed, not
-        buffered, so the fields have to be parsed before it arrives.
+        buffered, so the fields have to be parsed before it arrives. Currently
+        only diagnostic `similarity-search` with `parameters.query_smiles` is
+        accepted; distributed graph planning is not implemented.
       requestBody:
         required: true
         content:
@@ -388,7 +390,7 @@ components:
           type: array
           minItems: 1
           items: { type: string }
-          example: [similarity_search, similarity_graph]
+          example: [similarity-search]
         cpu_count:
           type: integer
           description: Accepted for forward compatibility; not yet persisted.
@@ -419,7 +421,7 @@ components:
       type: object
       required: [workload, input_uri, chunks]
       properties:
-        workload: { type: string, example: similarity_search }
+        workload: { type: string, example: similarity-search }
         input_uri: { type: string }
         parameters: { type: object, additionalProperties: true }
         chunks:
@@ -437,11 +439,11 @@ components:
       type: object
       required: [workload, file]
       properties:
-        workload: { type: string, example: similarity_search }
+        workload: { type: string, enum: [similarity-search], example: similarity-search }
         parameters:
           type: string
           description: JSON object, sent as a string form field.
-          example: '{"top_k":10}'
+          example: '{"query_smiles":"CCO","top_k":10}'
         chunk_rows:
           type: integer
           description: Data rows per shard. Default 1000.
@@ -486,11 +488,11 @@ components:
       type: object
       required: [worker_id]
       properties:
-        worker_id: { type: string }
+        worker_id: { type: string, format: uuid, description: Registered worker identity. }
         capabilities:
           type: array
           items: { type: string }
-          description: Workloads this worker can run. Empty means "any".
+          description: Accepted for compatibility only; registration capabilities decide eligibility.
         max_concurrency:
           type: integer
           description: Accepted; the coordinator leases one task per call.

docs/worker-daemon-task.md

@@ -59,7 +59,7 @@ Content-Type: application/json
 
 {
   "name": "lab-worker-01",
-  "capabilities": ["similarity-search", "similarity-graph"],
+  "capabilities": ["similarity-search"],
   "cpu_count": 8,
   "memory_mb": 16384
 }
@@ -74,8 +74,8 @@ POST /tasks/claim
 Content-Type: application/json
 
 {
-  "worker_id": "worker-01",
+  "worker_id": "<registered-uuid>",
-  "capabilities": ["similarity-search", "similarity-graph"],
+  "capabilities": ["similarity-search"],
   "max_concurrency": 1
 }
 ```
@@ -95,7 +95,7 @@ When a task is available, it returns `200 OK`:
     "sha256": "..."
   },
   "parameters": {
-    "query_id": "CHEMBL939",
+    "query_smiles": "CCO",
     "top_k": 20
   }
 }

scimesh/worker/cli.py

@@ -13,15 +13,17 @@ from .daemon import WorkerDaemon
 from .runners import SciMeshRunner
 
 
-def main(argv: list[str] | None = None) -> int:
+def build_parser() -> argparse.ArgumentParser:
+    """Build the worker CLI parser for command-line use and focused tests."""
     parser = argparse.ArgumentParser(
         prog="scimesh-worker",
         epilog=(
             "Environment: SCIMESH_COORDINATOR_URL, SCIMESH_WORK_DIR, "
             "SCIMESH_WORKER_NAME, SCIMESH_CPU_COUNT, SCIMESH_MEMORY_MB, "
             "SCIMESH_POLL_INTERVAL, SCIMESH_REQUEST_TIMEOUT, "
-            "SCIMESH_HEARTBEAT_INTERVAL, SCIMESH_CLEANUP_AFTER_SECONDS, and "
+            "SCIMESH_HEARTBEAT_INTERVAL, SCIMESH_CLEANUP_AFTER_SECONDS, "
-            "SCIMESH_BEARER_TOKEN. SCIMESH_WORKER_ID is a legacy/test override."
+            "SCIMESH_MAX_TASKS, and SCIMESH_BEARER_TOKEN. "
+            "SCIMESH_WORKER_ID is a legacy/test override."
         ),
     )
     parser.add_argument("--coordinator-url")
@@ -34,8 +36,31 @@ def main(argv: list[str] | None = None) -> int:
     parser.add_argument("--request-timeout", type=float)
     parser.add_argument("--heartbeat-interval", type=float)
     parser.add_argument("--cleanup-after-seconds", type=float)
+    lifecycle = parser.add_mutually_exclusive_group()
+    lifecycle.add_argument(
+        "--once",
+        action="store_true",
+        help="Claim at most one task, then exit; exit immediately when the queue is empty",
+    )
+    lifecycle.add_argument(
+        "--max-tasks",
+        type=int,
+        help="Process this many claimed tasks, then exit",
+    )
+    return parser
+
+
+def main(argv: list[str] | None = None) -> int:
+    parser = build_parser()
     args = parser.parse_args(argv)
-    overrides = {key: value for key, value in vars(args).items() if value is not None}
+    overrides = {
+        key: value
+        for key, value in vars(args).items()
+        if value is not None and key != "once"
+    }
+    if args.once:
+        overrides["max_tasks"] = 1
+        overrides["exit_when_idle"] = True
     if "work_dir" in overrides:
         overrides["work_dir"] = Path(overrides["work_dir"])
     try:
@@ -44,13 +69,13 @@ def main(argv: list[str] | None = None) -> int:
         parser.error(str(error))
     logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s %(message)s")
     client = HttpCoordinatorClient(config.coordinator_url, config.request_timeout, config.bearer_token)
-    WorkerDaemon(
+    completed_without_interruption = WorkerDaemon(
         config,
         client,
         HttpArtifactClient(config.coordinator_url, config.request_timeout, config.bearer_token),
         SciMeshRunner(),
     ).run_forever()
-    return 0
+    return 0 if completed_without_interruption else 130
 
 
 if __name__ == "__main__":

scimesh/worker/config.py

@@ -36,13 +36,16 @@ class WorkerConfig:
     heartbeat_interval: float = 15.0
     bearer_token: str | None = None
     cleanup_after_seconds: float | None = None
+    max_tasks: int | None = None
+    exit_when_idle: bool = False
+    # Distributed similarity-graph requires triangular block-pair planning and
+    # is deliberately not advertised until CTX-10. A normal worker must never
+    # make a multi-shard graph job appear scientifically complete.
     # The local CLI uses hyphens; the first coordinator contract used
-    # underscores. Advertise both stable spellings while jobs are migrated.
+    # underscores, so retain the search alias during migration.
     capabilities: tuple[str, ...] = (
         "similarity-search",
-        "similarity-graph",
         "similarity_search",
-        "similarity_graph",
     )
 
     def __post_init__(self) -> None:
@@ -66,6 +69,15 @@ class WorkerConfig:
         _positive_number(self.heartbeat_interval, "heartbeat_interval")
         if self.cleanup_after_seconds is not None:
             _positive_number(self.cleanup_after_seconds, "cleanup_after_seconds", allow_zero=True)
+        if self.max_tasks is not None:
+            if (
+                isinstance(self.max_tasks, bool)
+                or not isinstance(self.max_tasks, int)
+                or self.max_tasks < 1
+            ):
+                raise ValueError("max_tasks must be positive when set")
+        if not isinstance(self.exit_when_idle, bool):
+            raise ValueError("exit_when_idle must be a boolean")
         if not self.capabilities:
             raise ValueError("capabilities cannot be empty")
         # Runner subprocesses use a task directory as their cwd. Keep the
@@ -90,6 +102,7 @@ class WorkerConfig:
         cleanup = value("cleanup_after_seconds", "SCIMESH_CLEANUP_AFTER_SECONDS")
         cpu_count = value("cpu_count", "SCIMESH_CPU_COUNT", os.cpu_count() or 1)
         memory_mb = value("memory_mb", "SCIMESH_MEMORY_MB")
+        max_tasks = value("max_tasks", "SCIMESH_MAX_TASKS")
         return cls(
             coordinator_url=url.rstrip("/"),
             worker_id=value("worker_id", "SCIMESH_WORKER_ID"),
@@ -102,4 +115,6 @@ class WorkerConfig:
             heartbeat_interval=float(value("heartbeat_interval", "SCIMESH_HEARTBEAT_INTERVAL", "15")),
             bearer_token=value("bearer_token", "SCIMESH_BEARER_TOKEN"),
             cleanup_after_seconds=float(cleanup) if cleanup else None,
+            max_tasks=int(max_tasks) if max_tasks is not None else None,
+            exit_when_idle=bool(values.get("exit_when_idle", False)),
         )

scimesh/worker/daemon.py

@@ -4,8 +4,10 @@ from __future__ import annotations
 
 import logging
 from dataclasses import replace
+from dataclasses import dataclass
 from pathlib import Path
 import random
+import re
 import shutil
 import threading
 import time
@@ -72,6 +74,14 @@ class LeaseHeartbeat:
         return seconds
 
 
+@dataclass(frozen=True)
+class RunOnceOutcome:
+    """Whether a claim was made and whether that claimed task completed."""
+
+    claimed: bool
+    completed: bool
+
+
 class WorkerDaemon:
     def __init__(self, config: WorkerConfig, coordinator: CoordinatorClient, artifacts: ArtifactClient, runner: Runner) -> None:
         self.config, self.coordinator, self.artifacts, self.runner = config, coordinator, artifacts, runner
@@ -79,32 +89,68 @@ class WorkerDaemon:
         self._registered = False
         self.log = logging.getLogger("scimesh.worker")
 
-    def run_forever(self) -> None:
+    def run_forever(self) -> bool:
+        """Run until stopped; return false only when interrupted by the operator."""
         failures = 0
-        while True:
+        completed_tasks = 0
-            try:
+        self._log(
-                if not self._registered:
+            "started",
-                    self._register_worker()
+            max_tasks=self.config.max_tasks,
-                self._cleanup_expired_directories()
+            exit_when_idle=self.config.exit_when_idle,
-                claimed = self.run_once()
+        )
-                failures = 0
+        try:
-                if not claimed:
+            while True:
-                    self._sleep(self.config.poll_interval)
+                try:
-            except CoordinatorTransientError as error:
+                    if not self._registered:
-                failures += 1
+                        self._register_worker()
-                self._log("failed", error_type=type(error).__name__)
+                    self._cleanup_expired_directories()
-                self._sleep(min(self.config.poll_interval * 2 ** min(failures, 6), 60.0))
+                    outcome = self.run_once()
+                    failures = 0
+                    if outcome.claimed:
+                        if outcome.completed:
+                            completed_tasks += 1
+                        if self.config.exit_when_idle:
+                            self._log(
+                                "stopped",
+                                reason="one_claim_processed",
+                                completed_tasks=completed_tasks,
+                            )
+                            return True
+                        if (
+                            outcome.completed
+                            and self.config.max_tasks is not None
+                            and completed_tasks >= self.config.max_tasks
+                        ):
+                            self._log(
+                                "stopped",
+                                reason="max_tasks_reached",
+                                completed_tasks=completed_tasks,
+                            )
+                            return True
+                    elif self.config.exit_when_idle:
+                        self._log("stopped", reason="queue_empty", completed_tasks=completed_tasks)
+                        return True
+                    else:
+                        self._sleep(self.config.poll_interval)
+                except CoordinatorTransientError as error:
+                    failures += 1
+                    self._log("failed", error_type=type(error).__name__)
+                    self._sleep(min(self.config.poll_interval * 2 ** min(failures, 6), 60.0))
+        except KeyboardInterrupt:
+            self._log("stopped", reason="interrupted", completed_tasks=completed_tasks)
+            return False
 
-    def run_once(self) -> bool:
+    def run_once(self) -> RunOnceOutcome:
         worker_id = self._worker_id()
-        self._log("claiming")
+        self._log("claiming", log_level=logging.DEBUG)
         task = self.coordinator.claim(worker_id, self.config.capabilities)
         if task is None:
-            self._log("idle")
+            self._log("idle", log_level=logging.DEBUG)
-            return False
+            return RunOnceOutcome(claimed=False, completed=False)
         started = time.monotonic()
         task_dir = self.config.work_dir / task.task_id / str(task.attempt)
         heartbeat = LeaseHeartbeat(task, self.coordinator, self.config)
+        completed = False
         try:
             task_dir.mkdir(parents=True, exist_ok=False)
             heartbeat.start()
@@ -135,7 +181,15 @@ class WorkerDaemon:
                     },
                 },
             )
-            self._log("idle", task, elapsed_seconds=round(time.monotonic() - started, 3))
+            completed = True
+            self._log("completed", task, elapsed_seconds=round(time.monotonic() - started, 3))
+        except KeyboardInterrupt:
+            self._log("interrupted", task)
+            try:
+                self._report_failure(task, InterruptedError("worker interrupted by operator"))
+            except CoordinatorTransientError:
+                self._log("failed", task, error_type="FailureReportError")
+            raise
         except CoordinatorConflictError as error:
             self._log("lease_lost", task, error_type=type(error).__name__)
         except Exception as error:
@@ -143,10 +197,10 @@ class WorkerDaemon:
             self._report_failure(task, error)
         finally:
             heartbeat.stop()
-        return True
+        return RunOnceOutcome(claimed=True, completed=completed)
 
     def _report_failure(self, task: ClaimedTask, error: Exception) -> None:
-        message = str(error).replace(str(self.config.work_dir), "<worker-dir>")[:300]
+        message = self._sanitize_error_message(error)
         try:
             self.coordinator.fail(task, {"worker_id": self._worker_id(), "attempt": task.attempt, "error_code": type(error).__name__, "error_message": message})
         except CoordinatorTransientError:
@@ -154,6 +208,16 @@ class WorkerDaemon:
         except Exception:
             self._log("failed", task, error_type="FailureReportError")
 
+    def _sanitize_error_message(self, error: Exception) -> str:
+        """Keep coordinator-visible failures useful without exposing local paths."""
+        message = str(error).replace(str(self.config.work_dir), "<worker-dir>")
+        # CalledProcessError includes the complete argv, including sys.executable
+        # outside work_dir. Replace POSIX and Windows absolute paths before the
+        # message reaches the coordinator database or operator UI.
+        message = re.sub(r"(?<![\w:])[A-Za-z]:\\[^\s'\"\],)]+", "<path>", message)
+        message = re.sub(r"(?<![\w:])/(?:[^\s'\"\],)]+)", "<path>", message)
+        return message[:300]
+
     def _register_worker(self) -> None:
         registered = self.coordinator.register(
             self.config.worker_name,
@@ -180,9 +244,16 @@ class WorkerDaemon:
         """Keep completion payload exact: coordinator owns all artifact metadata."""
         return {"artifact_id": uploaded.artifact_id}
 
-    def _log(self, state: str, task: ClaimedTask | None = None, **extra: object) -> None:
+    def _log(
+        self,
+        state: str,
+        task: ClaimedTask | None = None,
+        *,
+        log_level: int = logging.INFO,
+        **extra: object,
+    ) -> None:
         fields = {"worker_id": self.config.worker_id, "task_id": task.task_id if task else None, "attempt": task.attempt if task else None, "state": state, **extra}
-        self.log.info("worker_event %s", fields)
+        self.log.log(log_level, "worker_event %s", fields)
 
     def _cleanup_expired_directories(self) -> None:
         """Remove only old task attempt directories when retention was configured."""

scripts/two-worker-smoke.sh

@@ -0,0 +1,165 @@
+#!/usr/bin/env bash
+#
+# End-to-end check: two Python workers process separate coordinator shards.
+#
+# Requires Docker, curl, python3, and an installed scimesh-worker (normally
+# from this repository's .venv). The test uses its own Compose project, ports,
+# volumes, and temporary worker directories, leaving a developer stack alone.
+
+set -euo pipefail
+
+ROOT_DIR=$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)
+COORDINATOR_DIR="$ROOT_DIR/coordinator"
+COMPOSE_PROJECT=${COMPOSE_PROJECT:-scimesh-two-worker-smoke}
+COORDINATOR_PORT=${COORDINATOR_PORT:-18081}
+POSTGRES_PORT=${POSTGRES_PORT:-55434}
+HOST="http://127.0.0.1:${COORDINATOR_PORT}"
+TOKEN=${SCIMESH_SMOKE_TOKEN:-two-worker-smoke-token}
+WORK_DIR=$(mktemp -d "${TMPDIR:-/tmp}/scimesh-two-worker-smoke.XXXXXX")
+WORKER_ONE_PID=""
+WORKER_TWO_PID=""
+WORKER_PYTHON=${SCIMESH_WORKER_PYTHON:-"$ROOT_DIR/.venv/bin/python"}
+
+cleanup() {
+    local exit_code=$?
+    if [[ "$exit_code" -ne 0 ]]; then
+        printf '\nTwo-worker smoke failed; worker logs follow.\n' >&2
+        sed -n '1,200p' "$WORK_DIR/worker-a.log" >&2 || true
+        sed -n '1,200p' "$WORK_DIR/worker-b.log" >&2 || true
+        (
+            cd "$COORDINATOR_DIR"
+            POSTGRES_PORT="$POSTGRES_PORT" COORDINATOR_PORT="$COORDINATOR_PORT" \
+                docker compose -p "$COMPOSE_PROJECT" logs coordinator >&2 || true
+        )
+    fi
+    if [[ -n "$WORKER_ONE_PID" ]]; then kill "$WORKER_ONE_PID" 2>/dev/null || true; fi
+    if [[ -n "$WORKER_TWO_PID" ]]; then kill "$WORKER_TWO_PID" 2>/dev/null || true; fi
+    if [[ -n "$WORKER_ONE_PID" ]]; then wait "$WORKER_ONE_PID" 2>/dev/null || true; fi
+    if [[ -n "$WORKER_TWO_PID" ]]; then wait "$WORKER_TWO_PID" 2>/dev/null || true; fi
+    (
+        cd "$COORDINATOR_DIR"
+        POSTGRES_PORT="$POSTGRES_PORT" COORDINATOR_PORT="$COORDINATOR_PORT" \
+            docker compose -p "$COMPOSE_PROJECT" down -v --remove-orphans >/dev/null 2>&1 || true
+    )
+    rm -rf "$WORK_DIR"
+    exit "$exit_code"
+}
+trap cleanup EXIT INT TERM
+
+require() {
+    command -v "$1" >/dev/null || {
+        printf 'missing required command: %s\n' "$1" >&2
+        exit 2
+    }
+}
+
+for command in docker curl python3; do require "$command"; done
+[[ -x "$WORKER_PYTHON" ]] || {
+    printf 'worker Python is not executable: %s\n' "$WORKER_PYTHON" >&2
+    printf 'Set SCIMESH_WORKER_PYTHON to a Python environment with SciMesh and RDKit.\n' >&2
+    exit 2
+}
+
+printf 'Starting isolated coordinator on %s (project %s)\n' "$HOST" "$COMPOSE_PROJECT"
+(
+    cd "$COORDINATOR_DIR"
+    POSTGRES_PORT="$POSTGRES_PORT" COORDINATOR_PORT="$COORDINATOR_PORT" \
+        WORKER_AUTH_TOKEN="$TOKEN" UI_AUTH_TOKEN= \
+        docker compose -p "$COMPOSE_PROJECT" up -d --build
+)
+
+for _ in $(seq 1 45); do
+    if curl -fsS "$HOST/health" >/dev/null; then break; fi
+    sleep 1
+done
+curl -fsS "$HOST/health" >/dev/null || {
+    printf 'coordinator did not become healthy\n' >&2
+    exit 1
+}
+
+start_worker() {
+    local worker_name=$1
+    local worker_dir=$2
+    SCIMESH_COORDINATOR_URL="$HOST" \
+        SCIMESH_BEARER_TOKEN="$TOKEN" \
+        SCIMESH_WORKER_NAME="$worker_name" \
+        SCIMESH_POLL_INTERVAL=0.2 \
+        "$WORKER_PYTHON" -m scimesh.worker.cli --work-dir "$worker_dir" --max-tasks 2 >"$worker_dir.log" 2>&1 &
+    STARTED_WORKER_PID=$!
+}
+
+start_worker two-worker-smoke-a "$WORK_DIR/worker-a"
+WORKER_ONE_PID=$STARTED_WORKER_PID
+start_worker two-worker-smoke-b "$WORK_DIR/worker-b"
+WORKER_TWO_PID=$STARTED_WORKER_PID
+
+for _ in $(seq 1 30); do
+    registered=$(docker compose -p "$COMPOSE_PROJECT" -f "$COORDINATOR_DIR/docker-compose.yml" \
+        exec -T postgres psql -U scimesh -d scimesh -Atc "SELECT count(*) FROM workers" 2>/dev/null || printf '0')
+    [[ "$registered" == "2" ]] && break
+    sleep 1
+done
+[[ "${registered:-0}" == "2" ]] || {
+    printf 'workers did not register; logs follow\n' >&2
+    sed -n '1,160p' "$WORK_DIR/worker-a.log" >&2 || true
+    sed -n '1,160p' "$WORK_DIR/worker-b.log" >&2 || true
+    exit 1
+}
+
+DATASET="$WORK_DIR/fixture.tsv"
+printf '%s\n' \
+    $'chembl_id\tcanonical_smiles' \
+    $'TEST001\tCC' $'TEST002\tCCC' $'TEST003\tCCCC' $'TEST004\tCCCO' $'TEST005\tCCN' \
+    $'TEST006\tCCCl' $'TEST007\tCCBr' $'TEST008\tCCF' $'TEST009\tCC=O' $'TEST010\tCC#N' \
+    $'TEST011\tCO' $'TEST012\tCOC' $'TEST013\tCOCC' $'TEST014\tCN' $'TEST015\tCNC' \
+    $'TEST016\tO=C=O' $'TEST017\tC1CC1' $'TEST018\tc1ccccc1' $'TEST019\tCC(C)O' $'TEST020\tCC(C)N' \
+    >"$DATASET"
+
+response=$(curl -fsS -H "Authorization: Bearer $TOKEN" -X POST "$HOST/jobs/upload" \
+    -F 'workload=similarity-search' \
+    -F 'parameters={"query_smiles":"CCO","top_k":5,"progress_every":0}' \
+    -F 'chunk_rows=5' \
+    -F 'max_rows=20' \
+    -F "file=@${DATASET};type=text/tab-separated-values")
+job_id=$(printf '%s' "$response" | python3 -c 'import json,sys; print(json.load(sys.stdin)["job_id"])')
+task_count=$(printf '%s' "$response" | python3 -c 'import json,sys; print(json.load(sys.stdin)["task_count"])')
+[[ "$task_count" == "4" ]] || {
+    printf 'expected four shards, got response: %s\n' "$response" >&2
+    exit 1
+}
+
+printf 'Submitted job %s with four shards\n' "$job_id"
+for _ in $(seq 1 90); do
+    job=$(curl -fsS -H "Authorization: Bearer $TOKEN" "$HOST/jobs/$job_id")
+    status=$(printf '%s' "$job" | python3 -c 'import json,sys; print(json.load(sys.stdin)["status"])')
+    [[ "$status" == "completed" || "$status" == "failed" || "$status" == "cancelled" ]] && break
+    sleep 1
+done
+
+printf '%s' "$job" | python3 -c '
+import json, sys
+job = json.load(sys.stdin)
+assert job["status"] == "completed", job
+assert job["total"] == 4, job
+assert job["completed"] == 4, job
+assert job["failed"] == 0, job
+'
+
+task_check=$(docker compose -p "$COMPOSE_PROJECT" -f "$COORDINATOR_DIR/docker-compose.yml" \
+    exec -T postgres psql -U scimesh -d scimesh -Atc \
+    "SELECT count(*) FROM tasks WHERE job_id = '$job_id'::uuid AND status = 'completed' AND attempt = 1 AND result_artifact_id IS NOT NULL")
+[[ "$task_check" == "4" ]] || {
+    printf 'expected four first-attempt tasks with coordinator artifacts, got %s\n' "$task_check" >&2
+    exit 1
+}
+
+worker_one_results=$(find "$WORK_DIR/worker-a" -name result.csv -type f | wc -l | tr -d ' ')
+worker_two_results=$(find "$WORK_DIR/worker-b" -name result.csv -type f | wc -l | tr -d ' ')
+[[ "$worker_one_results" -ge 1 && "$worker_two_results" -ge 1 ]] || {
+    printf 'both workers must process at least one shard (a=%s, b=%s)\n' \
+        "$worker_one_results" "$worker_two_results" >&2
+    exit 1
+}
+
+printf 'PASS: 4/4 shards completed; worker-a=%s, worker-b=%s\n' \
+    "$worker_one_results" "$worker_two_results"

tests/test_worker_daemon.py

@@ -1,7 +1,9 @@
 from __future__ import annotations
 
 import hashlib
+import logging
 from pathlib import Path
+import subprocess
 import time
 from datetime import datetime, timedelta, timezone
 from urllib.request import Request
@@ -9,8 +11,10 @@ from urllib.request import Request
 import pytest
 
 from scimesh.worker.config import WorkerConfig
+from scimesh.worker import cli as worker_cli
+from scimesh.worker.cli import build_parser
 from scimesh.worker.coordinator import CoordinatorTransientError
-from scimesh.worker.daemon import LeaseHeartbeat, WorkerDaemon
+from scimesh.worker.daemon import LeaseHeartbeat, RunOnceOutcome, WorkerDaemon
 from scimesh.worker.models import (
     ClaimedTask,
     InputArtifact,
@@ -92,7 +96,7 @@ def daemon(tmp_path: Path, task: ClaimedTask | None, content: bytes):
 def test_claims_runs_uploads_and_submits_csv(tmp_path: Path) -> None:
     content = b"input fixture"
     worker, coordinator, artifacts, runner, _ = daemon(tmp_path, make_task(content), content)
-    assert worker.run_once() is True
+    assert worker.run_once() == RunOnceOutcome(claimed=True, completed=True)
     assert runner.calls == 1
     assert len(artifacts.uploaded) == 1
     assert coordinator.heartbeats == [("task-1", 1, "worker-1")]
@@ -104,24 +108,153 @@ def test_claims_runs_uploads_and_submits_csv(tmp_path: Path) -> None:
 
 def test_no_task_does_not_create_directory(tmp_path: Path) -> None:
     worker, _, _, runner, config = daemon(tmp_path, None, b"")
-    assert worker.run_once() is False
+    assert worker.run_once() == RunOnceOutcome(claimed=False, completed=False)
     assert runner.calls == 0
     assert not config.work_dir.exists()
 
 
+def test_once_worker_exits_after_an_empty_claim(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
+    caplog.set_level(logging.INFO, logger="scimesh.worker")
+    worker, _, _, runner, _ = daemon(tmp_path, None, b"")
+    worker.config = WorkerConfig(**{**worker.config.__dict__, "exit_when_idle": True, "max_tasks": 1})
+    assert worker.run_forever() is True
+    assert runner.calls == 0
+    assert "queue_empty" in caplog.text
+
+
+def test_worker_stops_after_the_configured_number_of_claims(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
+    caplog.set_level(logging.INFO, logger="scimesh.worker")
+    content = b"input fixture"
+    worker, _, _, runner, _ = daemon(tmp_path, make_task(content), content)
+    worker.config = WorkerConfig(**{**worker.config.__dict__, "max_tasks": 1})
+    assert worker.run_forever() is True
+    assert runner.calls == 1
+    assert "max_tasks_reached" in caplog.text
+
+
+def test_keyboard_interrupt_stops_worker_without_propagating(tmp_path: Path, caplog: pytest.LogCaptureFixture) -> None:
+    caplog.set_level(logging.INFO, logger="scimesh.worker")
+    class InterruptingCoordinator(FakeCoordinator):
+        def claim(self, worker_id: str, capabilities: tuple[str, ...]) -> ClaimedTask | None:
+            raise KeyboardInterrupt
+
+    worker, _, _, _, _ = daemon(tmp_path, None, b"")
+    worker.coordinator = InterruptingCoordinator(None)
+    assert worker.run_forever() is False
+    assert "interrupted" in caplog.text
+
+
+def test_interrupting_an_active_task_reports_a_sanitized_failure(tmp_path: Path) -> None:
+    content = b"input fixture"
+    worker, coordinator, _, _, _ = daemon(tmp_path, make_task(content), content)
+
+    class InterruptingRunner(FakeRunner):
+        def run(self, task: ClaimedTask, task_dir: Path) -> RunResult:
+            raise KeyboardInterrupt
+
+    worker.runner = InterruptingRunner()
+    with pytest.raises(KeyboardInterrupt):
+        worker.run_once()
+    assert coordinator.failures == [
+        {
+            "worker_id": "worker-1",
+            "attempt": 1,
+            "error_code": "InterruptedError",
+            "error_message": "worker interrupted by operator",
+        }
+    ]
+
+
+def test_max_tasks_counts_successes_not_failed_claims(tmp_path: Path) -> None:
+    successful_content = b"successful input"
+
+    class SequencedCoordinator(FakeCoordinator):
+        def __init__(self) -> None:
+            super().__init__(None)
+            self.tasks = [
+                make_task(b"bad input", "wrong-checksum"),
+                ClaimedTask(
+                    "task-2",
+                    1,
+                    (datetime.now(timezone.utc) + timedelta(seconds=60)).isoformat(),
+                    "similarity-search",
+                    InputArtifact(
+                        "https://example.test/input",
+                        hashlib.sha256(successful_content).hexdigest(),
+                    ),
+                    {"query_id": "CHEMBL1"},
+                ),
+            ]
+
+        def claim(self, worker_id: str, capabilities: tuple[str, ...]) -> ClaimedTask | None:
+            return self.tasks.pop(0) if self.tasks else None
+
+    coordinator = SequencedCoordinator()
+    artifacts, runner = FakeArtifacts(successful_content), FakeRunner()
+    config = WorkerConfig("https://example.test", "worker-1", tmp_path / "work", max_tasks=1)
+    worker = WorkerDaemon(config, coordinator, artifacts, runner)
+    assert worker.run_forever() is True
+    assert len(coordinator.failures) == 1
+    assert len(coordinator.submissions) == 1
+    assert runner.calls == 1
+
+
+def test_worker_cli_lifecycle_options_are_explicit_and_exclusive() -> None:
+    parser = build_parser()
+    assert parser.parse_args(["--once"]).once is True
+    assert parser.parse_args(["--max-tasks", "2"]).max_tasks == 2
+    with pytest.raises(SystemExit):
+        parser.parse_args(["--once", "--max-tasks", "2"])
+
+
+def test_worker_cli_uses_a_nonzero_exit_code_for_interruption(
+    monkeypatch: pytest.MonkeyPatch, tmp_path: Path
+) -> None:
+    class InterruptedDaemon:
+        def __init__(self, *_: object) -> None:
+            pass
+
+        def run_forever(self) -> bool:
+            return False
+
+    monkeypatch.setattr(worker_cli, "WorkerDaemon", InterruptedDaemon)
+    assert worker_cli.main(
+        ["--coordinator-url", "https://example.test", "--work-dir", str(tmp_path)]
+    ) == 130
+
+
+@pytest.mark.parametrize("value", [0, -1, True])
+def test_max_tasks_must_be_positive(value: object, tmp_path: Path) -> None:
+    with pytest.raises(ValueError, match="max_tasks"):
+        WorkerConfig("https://example.test", None, tmp_path, max_tasks=value)  # type: ignore[arg-type]
+
+
 def test_bad_checksum_reports_failure_without_running(tmp_path: Path) -> None:
     worker, coordinator, _, runner, _ = daemon(tmp_path, make_task(b"actual", "not-the-hash"), b"actual")
-    assert worker.run_once() is True
+    assert worker.run_once() == RunOnceOutcome(claimed=True, completed=False)
     assert runner.calls == 0
     assert coordinator.failures[0]["error_code"] == "ValueError"
     assert not coordinator.submissions
 
 
+def test_failure_reporting_removes_paths_outside_the_worker_directory(tmp_path: Path) -> None:
+    worker, coordinator, _, _, _ = daemon(tmp_path, make_task(b"input"), b"input")
+    error = subprocess.CalledProcessError(
+        1,
+        ["/home/alice/.venv/bin/python", "-m", "scimesh.cli", "/private/input.tsv"],
+    )
+    worker._report_failure(make_task(b"input"), error)
+    message = coordinator.failures[0]["error_message"]
+    assert "/home/alice" not in message
+    assert "/private/input.tsv" not in message
+    assert "<path>" in message
+
+
 def test_directory_creation_failure_is_reported(tmp_path: Path) -> None:
     content = b"input fixture"
     worker, coordinator, _, _, config = daemon(tmp_path, make_task(content), content)
     (config.work_dir / "task-1" / "1").mkdir(parents=True)
-    assert worker.run_once() is True
+    assert worker.run_once() == RunOnceOutcome(claimed=True, completed=False)
     assert coordinator.failures[0]["error_code"] == "FileExistsError"
 
 
@@ -312,6 +445,7 @@ def test_environment_overrides_allow_cli_only_configuration(monkeypatch: pytest.
     assert config.worker_id is None
     assert "similarity-search" in config.capabilities
     assert "similarity_search" in config.capabilities
+    assert "similarity-graph" not in config.capabilities
 
 
 def test_relative_work_dir_is_normalized_for_runner_subprocesses(