Phase 3: Results visualization, jury pipeline, job management, and performance

- Add complete jury/voting visualization: concordance chart, 3-column confusion
  matrices with rejection class highlighted in gold, sample predictions dot plot,
  vote matrix heatmap, FBM stats, jury vs best individual comparison
- Update all chart colors to predomicspkg defaults (deepskyblue/firebrick) with
  transparent fills and fine grid on heatmaps
- Replace box plots with violin plots (points='all', jitter, meanline)
- Add job table enhancements: search, pagination (10/page), config hash+summary
  column, sortable disk size column, duration, user tracking
- Add duplicate job detection with config hash normalization (strip nulls)
- Cache disk_size_bytes in DB (v8 migration) to avoid per-request directory walks
- Population table: pagination 10/page, features sorted by group (neg/pos)
- Feature prevalence sorted decreasing (most prevalent at top)
- Add shared chart theme composable (useChartTheme.js)
- Add MSP annotation service for feature labels
- All 110 tests passing, 50% code coverage

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: eprifti

.gitignore

@@ -28,6 +28,7 @@ Thumbs.db
 # Data & uploads (runtime)
 data/uploads/
 data/projects/
+data/cache/
 backend/data/
 *.db
 

Dockerfile

@@ -22,6 +22,7 @@ ENV PATH="/root/.cargo/bin:${PATH}"
 RUN pip install --no-cache-dir maturin
 
 WORKDIR /build
+COPY gpredomics/ ./gpredomics/
 COPY gpredomicspy/ ./gpredomicspy/
 RUN cd gpredomicspy && maturin build --release --out /build/wheels
 

backend/app/main.py

@@ -464,6 +464,141 @@ async def _migrate_add_admin_flag(conn):
     _log.info("Migration v4_admin_flag complete")
 
 
+async def _migrate_add_job_name(conn):
+    """v5: Add name column to jobs table. Idempotent."""
+    try:
+        r = await conn.execute(
+            text("SELECT 1 FROM schema_versions WHERE version = 'v5_job_name'")
+        )
+        if r.scalar():
+            return
+    except Exception:
+        pass
+
+    _log.info("Migration v5: job name — starting")
+
+    try:
+        r = await conn.execute(text(
+            "SELECT column_name FROM information_schema.columns "
+            "WHERE table_name = 'jobs' AND column_name = 'name'"
+        ))
+        if not r.scalar():
+            await conn.execute(text(
+                "ALTER TABLE jobs ADD COLUMN name VARCHAR(255)"
+            ))
+            _log.info("  Added jobs.name column")
+    except Exception:
+        pass
+
+    await conn.execute(text(
+        "INSERT INTO schema_versions (version, applied_at) "
+        "VALUES ('v5_job_name', CURRENT_TIMESTAMP) ON CONFLICT DO NOTHING"
+    ))
+    _log.info("Migration v5_job_name complete")
+
+
+async def _migrate_add_job_user_id(conn):
+    """v6: Add user_id FK to jobs table for tracking who launched each job."""
+    try:
+        r = await conn.execute(
+            text("SELECT 1 FROM schema_versions WHERE version = 'v6_job_user_id'")
+        )
+        if r.scalar():
+            return
+    except Exception:
+        pass
+
+    _log.info("Migration v6: job user_id — starting")
+
+    try:
+        r = await conn.execute(text(
+            "SELECT column_name FROM information_schema.columns "
+            "WHERE table_name = 'jobs' AND column_name = 'user_id'"
+        ))
+        if not r.scalar():
+            await conn.execute(text(
+                "ALTER TABLE jobs ADD COLUMN user_id VARCHAR(12) REFERENCES users(id) ON DELETE SET NULL"
+            ))
+            _log.info("  Added jobs.user_id column")
+    except Exception:
+        pass
+
+    await conn.execute(text(
+        "INSERT INTO schema_versions (version, applied_at) "
+        "VALUES ('v6_job_user_id', CURRENT_TIMESTAMP) ON CONFLICT DO NOTHING"
+    ))
+    _log.info("Migration v6_job_user_id complete")
+
+
+async def _migrate_add_job_config_hash(conn):
+    """v7: Add config_hash column to jobs for duplicate detection."""
+    try:
+        r = await conn.execute(
+            text("SELECT 1 FROM schema_versions WHERE version = 'v7_job_config_hash'")
+        )
+        if r.scalar():
+            return
+    except Exception:
+        pass
+
+    _log.info("Migration v7: job config_hash — starting")
+
+    try:
+        r = await conn.execute(text(
+            "SELECT column_name FROM information_schema.columns "
+            "WHERE table_name = 'jobs' AND column_name = 'config_hash'"
+        ))
+        if not r.scalar():
+            await conn.execute(text(
+                "ALTER TABLE jobs ADD COLUMN config_hash VARCHAR(32)"
+            ))
+            await conn.execute(text(
+                "CREATE INDEX IF NOT EXISTS ix_jobs_config_hash ON jobs (config_hash)"
+            ))
+            _log.info("  Added jobs.config_hash column with index")
+    except Exception:
+        pass
+
+    await conn.execute(text(
+        "INSERT INTO schema_versions (version, applied_at) "
+        "VALUES ('v7_job_config_hash', CURRENT_TIMESTAMP) ON CONFLICT DO NOTHING"
+    ))
+    _log.info("Migration v7_job_config_hash complete")
+
+
+async def _migrate_add_job_disk_size(conn):
+    """v8: Add disk_size_bytes column to jobs for cached disk usage."""
+    try:
+        r = await conn.execute(
+            text("SELECT 1 FROM schema_versions WHERE version = 'v8_job_disk_size'")
+        )
+        if r.scalar():
+            return
+    except Exception:
+        pass
+
+    _log.info("Migration v8: job disk_size_bytes — starting")
+
+    try:
+        r = await conn.execute(text(
+            "SELECT column_name FROM information_schema.columns "
+            "WHERE table_name = 'jobs' AND column_name = 'disk_size_bytes'"
+        ))
+        if not r.scalar():
+            await conn.execute(text(
+                "ALTER TABLE jobs ADD COLUMN disk_size_bytes BIGINT"
+            ))
+            _log.info("  Added jobs.disk_size_bytes column")
+    except Exception:
+        pass
+
+    await conn.execute(text(
+        "INSERT INTO schema_versions (version, applied_at) "
+        "VALUES ('v8_job_disk_size', CURRENT_TIMESTAMP) ON CONFLICT DO NOTHING"
+    ))
+    _log.info("Migration v8_job_disk_size complete")
+
+
 @asynccontextmanager
 async def lifespan(app: FastAPI):
     """Startup/shutdown events."""
@@ -478,6 +613,14 @@ async def lifespan(app: FastAPI):
         await _migrate_to_composite_datasets(conn)
     async with engine.begin() as conn:
         await _migrate_add_admin_flag(conn)
+    async with engine.begin() as conn:
+        await _migrate_add_job_name(conn)
+    async with engine.begin() as conn:
+        await _migrate_add_job_user_id(conn)
+    async with engine.begin() as conn:
+        await _migrate_add_job_config_hash(conn)
+    async with engine.begin() as conn:
+        await _migrate_add_job_disk_size(conn)
     _log.info("PredomicsApp started — data_dir=%s", settings.data_dir)
     yield
 

backend/app/models/db_models.py

@@ -96,14 +96,19 @@ class Job(Base):
 
     id: Mapped[str] = mapped_column(String(12), primary_key=True, default=_new_id)
     project_id: Mapped[str] = mapped_column(ForeignKey("projects.id", ondelete="CASCADE"), nullable=False)
+    user_id: Mapped[Optional[str]] = mapped_column(ForeignKey("users.id", ondelete="SET NULL"), nullable=True)
+    name: Mapped[Optional[str]] = mapped_column(String(255), nullable=True)
     status: Mapped[str] = mapped_column(String(20), default="pending")
     config: Mapped[Optional[dict]] = mapped_column(JSON, nullable=True)
     results_path: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
     error_message: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
     created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=_utcnow)
     completed_at: Mapped[Optional[datetime]] = mapped_column(DateTime(timezone=True), nullable=True)
+    config_hash: Mapped[Optional[str]] = mapped_column(String(32), nullable=True, index=True)
+    disk_size_bytes: Mapped[Optional[int]] = mapped_column(nullable=True)
 
     project: Mapped["Project"] = relationship(back_populates="jobs")
+    owner: Mapped[Optional["User"]] = relationship()
 
 
 class ProjectShare(Base):

backend/app/models/schemas.py

@@ -182,6 +182,7 @@ class PopulationResponse(BaseModel):
 
 class ExperimentSummary(BaseModel):
     job_id: str
+    name: Optional[str] = None
     status: JobStatus
     fold_count: int = 0
     generation_count: int = 0
@@ -190,6 +191,16 @@ class ExperimentSummary(BaseModel):
     sample_count: int = 0
     best_auc: Optional[float] = None
     best_k: Optional[int] = None
+    created_at: Optional[str] = None
+    completed_at: Optional[str] = None
+    duration_seconds: Optional[float] = None
+    config_summary: Optional[str] = None
+    user_name: Optional[str] = None
+    language: Optional[str] = None
+    data_type: Optional[str] = None
+    population_size: Optional[int] = None
+    config_hash: Optional[str] = None
+    disk_size_bytes: Optional[int] = None
 
 
 class ExperimentDetail(ExperimentSummary):

backend/app/routers/admin.py

@@ -1,14 +1,20 @@
-"""Admin endpoints: user management."""
+"""Admin endpoints: user management and default configuration."""
+
+import json
+from pathlib import Path
 
 from fastapi import APIRouter, Depends, HTTPException
 from sqlalchemy import select, func
 from sqlalchemy.ext.asyncio import AsyncSession
 
+from ..core.config import settings
 from ..core.database import get_db
 from ..core.deps import get_admin_user
 from ..models.db_models import User, Project, Dataset
 from ..models.auth_schemas import AdminUserResponse, AdminUserUpdate
 
+DEFAULTS_PATH = Path(settings.data_dir) / "admin_defaults.json"
+
 router = APIRouter(prefix="/admin", tags=["admin"])
 
 
@@ -114,3 +120,42 @@ async def delete_user(
 
     await db.delete(target)
     return {"status": "deleted", "email": target.email}
+
+
+def _load_defaults() -> dict:
+    """Load admin defaults from disk."""
+    if DEFAULTS_PATH.exists():
+        return json.loads(DEFAULTS_PATH.read_text())
+    return {}
+
+
+def _save_defaults(data: dict) -> None:
+    """Save admin defaults to disk."""
+    DEFAULTS_PATH.parent.mkdir(parents=True, exist_ok=True)
+    DEFAULTS_PATH.write_text(json.dumps(data, indent=2))
+
+
+@router.get("/defaults")
+async def get_defaults(admin: User = Depends(get_admin_user)):
+    """Get the admin default parameter overrides (admin only)."""
+    return _load_defaults()
+
+
+@router.get("/defaults/public")
+async def get_defaults_public():
+    """Get the admin default parameter overrides (public, no auth required).
+
+    Used by the Parameters form to show current server defaults.
+    """
+    return _load_defaults()
+
+
+@router.put("/defaults")
+async def set_defaults(body: dict, admin: User = Depends(get_admin_user)):
+    """Set admin default parameter overrides (admin only).
+
+    Accepts a flat dict of section.key overrides, e.g.:
+    {"general.language": "bin,ter", "ga.population_size": 3000, "voting.vote": true}
+    """
+    _save_defaults(body)
+    return body