feat: add research_api database and core models (Project, Intent, PaperAsset, ClaimAsset, Source, FeedItem)

folder_paths.py

@@ -494,3 +494,19 @@ def get_input_subfolders() -> list[str]:
         return sorted(folders)
     except FileNotFoundError:
         return []
+
+
+# Research Workbench paths
+RESEARCH_PATHS = {
+    "papers": "research_workbench/assets/papers",
+    "datasets": "research_workbench/assets/datasets",
+    "code": "research_workbench/assets/code",
+    "experiments": "research_workbench/assets/experiments",
+    "figures": "research_workbench/assets/figures",
+    "styles": "research_workbench/assets/styles",
+    "claims": "research_workbench/assets/claims",
+    "reviews": "research_workbench/assets/reviews",
+    "projects": "research_workbench/projects",
+    "inbox": "research_workbench/inbox",
+    "exports": "research_workbench/exports",
+}

research_api/db.py

@@ -0,0 +1,28 @@
+"""Research Workbench database session management."""
+from pathlib import Path
+from sqlalchemy import create_engine
+from sqlalchemy.orm import sessionmaker
+from sqlalchemy.pool import StaticPool
+
+_COMFYUI_ROOT = Path(__file__).parent.parent
+_DB_PATH = _COMFYUI_ROOT / "research_workbench.db"
+
+DATABASE_URL = f"sqlite:///{_DB_PATH}"
+
+engine = create_engine(
+    DATABASE_URL,
+    connect_args={"check_same_thread": False},
+    poolclass=StaticPool,
+)
+session_maker = sessionmaker(bind=engine)
+
+
+def create_session():
+    """Create a new database session."""
+    return session_maker()
+
+
+def init_db():
+    """Create all research tables."""
+    from research_api.models import Base
+    Base.metadata.create_all(engine)

research_api/models.py

@@ -0,0 +1,126 @@
+"""Research Workbench SQLAlchemy models."""
+import uuid
+from datetime import datetime
+from sqlalchemy import Column, String, Float, Integer, DateTime, Boolean, ForeignKey, Text, JSON
+from sqlalchemy.orm import relationship
+import app.database.models as models
+
+Base = models.Base
+
+
+def new_id():
+    return str(uuid.uuid4())
+
+
+class Project(Base):
+    __tablename__ = "projects"
+
+    id = Column(String, primary_key=True, default=new_id)
+    title = Column(String, nullable=False)
+    goal = Column(String, nullable=True)
+    current_direction = Column(String, nullable=True)
+    status = Column(String, default="active")  # active, paused, completed
+    last_active_at = Column(DateTime, nullable=True)
+    created_at = Column(DateTime, default=datetime.utcnow)
+    updated_at = Column(DateTime, default=datetime.utcnow, onupdate=datetime.utcnow)
+
+    intents = relationship("Intent", back_populates="project")
+
+
+class Intent(Base):
+    __tablename__ = "intents"
+
+    id = Column(String, primary_key=True, default=new_id)
+    project_id = Column(String, ForeignKey("projects.id"), nullable=False)
+    intent_type = Column(String, nullable=False)  # LiteratureTracking, Writing, ReviewRebuttal
+    title = Column(String, nullable=False)
+    goal = Column(String, nullable=True)
+    status = Column(String, default="active")  # active, paused, blocked, completed
+    priority = Column(Integer, default=1)
+    next_action = Column(String, nullable=True)
+    risk_flags = Column(JSON, nullable=True)  # List stored as JSON
+    created_at = Column(DateTime, default=datetime.utcnow)
+    updated_at = Column(DateTime, default=datetime.utcnow, onupdate=datetime.utcnow)
+
+    project = relationship("Project", back_populates="intents")
+
+
+class PaperAsset(Base):
+    __tablename__ = "paper_assets"
+
+    id = Column(String, primary_key=True, default=new_id)
+    title = Column(String, nullable=False)
+    authors_text = Column(String, nullable=True)
+    journal_or_source = Column(String, nullable=True)
+    published_at = Column(String, nullable=True)
+    doi = Column(String, nullable=True)
+    abstract = Column(Text, nullable=True)
+    source_url = Column(String, nullable=True)
+    pdf_url = Column(String, nullable=True)
+    local_pdf_path = Column(String, nullable=True)
+    quick_read_summary = Column(Text, nullable=True)
+    why_relevant = Column(Text, nullable=True)
+    potential_use = Column(Text, nullable=True)
+    read_status = Column(String, default="unread")  # unread, quick-reviewed, skimmed, deeply-read
+    library_status = Column(String, default="pending")  # pending, library
+    style_candidate = Column(Boolean, default=False)
+    created_at = Column(DateTime, default=datetime.utcnow)
+    updated_at = Column(DateTime, default=datetime.utcnow, onupdate=datetime.utcnow)
+
+
+class ClaimAsset(Base):
+    __tablename__ = "claim_assets"
+
+    id = Column(String, primary_key=True, default=new_id)
+    project_id = Column(String, ForeignKey("projects.id"), nullable=False)
+    claim_text = Column(Text, nullable=False)
+    claim_type = Column(String, nullable=True)  # performance, robustness, generalization
+    support_level = Column(String, default="unsupported")  # unsupported, weakly_supported, partially_supported, supported, contested
+    supporting_experiment_refs = Column(JSON, nullable=True)
+    supporting_figure_refs = Column(JSON, nullable=True)
+    supporting_paper_refs = Column(JSON, nullable=True)
+    linked_sections = Column(JSON, nullable=True)
+    open_caveats = Column(Text, nullable=True)
+    status = Column(String, default="draft")  # draft, partially-supported, supported, disputed, removed
+    created_at = Column(DateTime, default=datetime.utcnow)
+    updated_at = Column(DateTime, default=datetime.utcnow, onupdate=datetime.utcnow)
+
+
+class Source(Base):
+    __tablename__ = "sources"
+
+    id = Column(String, primary_key=True, default=new_id)
+    name = Column(String, nullable=False)
+    category = Column(String, nullable=True)  # journal, arxiv, conference
+    intake_type = Column(String, default="rss")  # rss, toc, api
+    feed_url = Column(String, nullable=True)
+    site_url = Column(String, nullable=True)
+    priority = Column(Integer, default=1)
+    enabled = Column(Boolean, default=True)
+    include_in_brief = Column(Boolean, default=True)
+    allow_pdf_attempt = Column(Boolean, default=False)
+    topic_bias = Column(JSON, nullable=True)
+    notes = Column(Text, nullable=True)
+    created_at = Column(DateTime, default=datetime.utcnow)
+    updated_at = Column(DateTime, default=datetime.utcnow, onupdate=datetime.utcnow)
+
+
+class FeedItem(Base):
+    __tablename__ = "feed_items"
+
+    id = Column(String, primary_key=True, default=new_id)
+    source_id = Column(String, ForeignKey("sources.id"), nullable=True)
+    external_key = Column(String, nullable=True)
+    title = Column(String, nullable=False)
+    authors_text = Column(String, nullable=True)
+    published_at = Column(String, nullable=True)
+    abstract = Column(Text, nullable=True)
+    source_url = Column(String, nullable=True)
+    pdf_url = Column(String, nullable=True)
+    doi = Column(String, nullable=True)
+    rank_score = Column(Float, default=0.0)
+    novelty_score = Column(Float, default=0.0)
+    transferability_score = Column(Float, default=0.0)
+    status = Column(String, default="discovered")  # discovered, ranked, presented, quick-reviewed, saved, ignored
+    created_at = Column(DateTime, default=datetime.utcnow)
+    updated_at = Column(DateTime, default=datetime.utcnow, onupdate=datetime.utcnow)