use dedicated database for advisories

src/seclab_taskflows/mcp_servers/ghsa.py

@@ -1,3 +1,6 @@
+# SPDX-FileCopyrightText: GitHub, Inc.
+# SPDX-License-Identifier: MIT
+
 import logging
 
 from fastmcp import FastMCP
@@ -6,7 +9,12 @@
 import json
 from urllib.parse import urlparse, parse_qs
 from .gh_code_scanning import call_api
-from seclab_taskflow_agent.path_utils import log_file_name
+from seclab_taskflow_agent.path_utils import mcp_data_dir, log_file_name
+from .ghsa_models import GHSA, GHSASummary, Base
+from pathlib import Path
+from sqlalchemy import create_engine
+from sqlalchemy.orm import Session
+from .utils import process_repo
 
 logging.basicConfig(
     level=logging.DEBUG,
@@ -17,17 +25,150 @@
 
 mcp = FastMCP("GitHubRepoAdvisories")
 
+MEMORY = mcp_data_dir("seclab-taskflows", "ghsa", "GHSA_DIR")
+
+
+def ghsa_to_dict(result):
+    return {
+        "id": result.id,
+        "ghsa_id": result.ghsa_id,
+        "repo": result.repo.lower(),
+        "severity": result.severity,
+        "cve_id": result.cve_id,
+        "description": result.description,
+        "summary": result.summary,
+        "published_at": result.published_at,
+        "state": result.state,
+    }
+
+
+def ghsa_summary_to_dict(summary):
+    return {
+        "id": summary.id,
+        "repo": summary.repo.lower(),
+        "total_advisories": summary.total_advisories,
+        "high_severity_count": summary.high_severity_count,
+        "medium_severity_count": summary.medium_severity_count,
+        "low_severity_count": summary.low_severity_count,
+        "summary_notes": summary.summary_notes,
+    }
+
+class GHSABackend:
+    def __init__(self, db_dir: str):
+        # Directory in which the GHSA SQLite database file will be stored.
+        self.db_dir = db_dir
+        db_uri = "sqlite://" if not Path(self.db_dir).exists() else f"sqlite:///{self.db_dir}/ghsa.db"
+        self.engine = create_engine(db_uri, echo=False)
+        Base.metadata.create_all(
+            self.engine,
+            tables=[
+                GHSA.__table__,
+                GHSASummary.__table__,
+            ],
+        )
+
+    def store_new_ghsa(self, repo, ghsa_id, severity, cve_id, description, summary, published_at, state):
+        with Session(self.engine) as session:
+            existing = session.query(GHSA).filter_by(repo=repo, ghsa_id=ghsa_id).first()
+            if existing:
+                if severity:
+                    existing.severity = severity
+                if cve_id:
+                    existing.cve_id = cve_id
+                if description:
+                    existing.description = description
+                if summary:
+                    existing.summary = summary
+                if published_at:
+                    existing.published_at = published_at
+                if state:
+                    existing.state = state
+            else:
+                new_ghsa = GHSA(
+                    repo=repo,
+                    ghsa_id=ghsa_id,
+                    severity=severity,
+                    cve_id=cve_id,
+                    description=description,
+                    summary=summary,
+                    published_at=published_at,
+                    state=state,
+                )
+                session.add(new_ghsa)
+            session.commit()
+        return f"Updated or added GHSA {ghsa_id} for {repo}"
+
+    def get_ghsa(self, repo, ghsa_id):
+        with Session(self.engine) as session:
+            existing = session.query(GHSA).filter_by(repo=repo, ghsa_id=ghsa_id).first()
+        if not existing:
+            return None
+        return ghsa_to_dict(existing)
+
+    def get_ghsas(self, repo):
+        with Session(self.engine) as session:
+            existing = session.query(GHSA).filter_by(repo=repo).all()
+        return [ghsa_to_dict(ghsa) for ghsa in existing]
+
+    def store_new_ghsa_summary(
+        self,
+        repo,
+        total_advisories,
+        high_severity_count,
+        medium_severity_count,
+        low_severity_count,
+        summary_notes,
+    ):
+        with Session(self.engine) as session:
+            existing = session.query(GHSASummary).filter_by(repo=repo).first()
+            if existing:
+                existing.total_advisories = total_advisories
+                existing.high_severity_count = high_severity_count
+                existing.medium_severity_count = medium_severity_count
+                existing.low_severity_count = low_severity_count
+                existing.summary_notes = summary_notes
+            else:
+                new_summary = GHSASummary(
+                    repo=repo,
+                    total_advisories=total_advisories,
+                    high_severity_count=high_severity_count,
+                    medium_severity_count=medium_severity_count,
+                    low_severity_count=low_severity_count,
+                    summary_notes=summary_notes,
+                )
+                session.add(new_summary)
+            session.commit()
+        return f"Updated or added GHSA summary for {repo}"
+
+    def get_ghsa_summary(self, repo):
+        with Session(self.engine) as session:
+            existing = session.query(GHSASummary).filter_by(repo=repo).first()
+        if not existing:
+            return None
+        return ghsa_summary_to_dict(existing)
+
+    def clear_repo(self, repo):
+        with Session(self.engine) as session:
+            session.query(GHSA).filter_by(repo=repo).delete()
+            session.query(GHSASummary).filter_by(repo=repo).delete()
+            session.commit()
+        return f"Cleared GHSA results for repo {repo}"
+
+
+backend = GHSABackend(MEMORY)
 
 # The advisories contain a lot of information, so we need to filter
 # some of it out to avoid exceeding the maximum prompt size.
 def parse_advisory(advisory: dict) -> dict:
     logging.debug(f"advisory: {advisory}")
     return {
-        "ghsa_id": advisory.get("ghsa_id", ""),
-        "cve_id": advisory.get("cve_id", ""),
-        "summary": advisory.get("summary", ""),
-        "published_at": advisory.get("published_at", ""),
-        "state": advisory.get("state", ""),
+        "ghsa_id": advisory.get("ghsa_id") or "",
+        "cve_id": advisory.get("cve_id") or "",
+        "summary": advisory.get("summary") or "",
+        "description": advisory.get("description") or "",
+        "severity": advisory.get("severity") or "",
+        "published_at": advisory.get("published_at") or "",
+        "state": advisory.get("state") or "",
     }
 
 
@@ -70,6 +211,132 @@ async def fetch_GHSA_list(
         return results
     return json.dumps(results, indent=2)
 
+@mcp.tool()
+async def fetch_and_store_GHSA_list(
+    owner: str = Field(description="The owner of the repo"), repo: str = Field(description="The repository name"),
+    return_results: bool = Field(description="Whether to return the fetched results as a JSON string", default=False)
+) -> str:
+    """Fetch all GitHub Security Advisories (GHSAs) for a specific repository and store them in the database."""
+    results = await fetch_GHSA_list_from_gh(owner, repo)
+    if isinstance(results, str):
+        return results
+    for advisory in results:
+        backend.store_new_ghsa(
+            process_repo(owner, repo),
+            advisory["ghsa_id"],
+            advisory["severity"],
+            advisory["cve_id"],
+            advisory["description"],
+            advisory["summary"],
+            advisory["published_at"],
+            advisory["state"],
+        )
+    if return_results:
+        return json.dumps(results, indent=2)
+    return f"Fetched and stored {len(results)} GHSAs for {owner}/{repo}"
+
+@mcp.tool()
+def store_new_ghsa(
+    owner: str = Field(description="The owner of the GitHub repository"),
+    repo: str = Field(description="The name of the GitHub repository"),
+    ghsa_id: str = Field(description="The GHSA ID of the advisory"),
+    severity: str = Field(description="The severity of the advisory"),
+    cve_id: str = Field(description="The CVE ID if available", default=""),
+    description: str = Field(description="Description for this advisory", default=""),
+    summary: str = Field(description="Summary for this advisory", default=""),
+    published_at: str = Field(description="Published timestamp for this advisory", default=""),
+    state: str = Field(description="State for this advisory (e.g. published, withdrawn)", default=""),
+):
+    """Store a GHSA advisory record in the database."""
+    return backend.store_new_ghsa(
+        process_repo(owner, repo), ghsa_id, severity, cve_id, description, summary, published_at, state
+    )
+
+@mcp.tool()
+def get_ghsa_from_db(
+    owner: str = Field(description="The owner of the GitHub repository"),
+    repo: str = Field(description="The name of the GitHub repository"),
+    ghsa_id: str = Field(description="The GHSA ID of the advisory"),
+):
+    """Get a GHSA advisory record from the database."""
+    repo_name = process_repo(owner, repo)
+    result = backend.get_ghsa(repo_name, ghsa_id)
+    if not result:
+        return f"Error: No GHSA entry exists in repo: {repo_name} and ghsa_id {ghsa_id}"
+    return json.dumps(result)
+
+
+@mcp.tool()
+def get_ghsas_for_repo_from_db(
+    owner: str = Field(description="The owner of the GitHub repository"),
+    repo: str = Field(description="The name of the GitHub repository"),
+):
+    """Get all GHSA advisory records for a repository."""
+    return json.dumps(backend.get_ghsas(process_repo(owner, repo)))
+
+@mcp.tool()
+def store_new_ghsa_summary(
+    owner: str = Field(description="The owner of the GitHub repository"),
+    repo: str = Field(description="The name of the GitHub repository"),
+    total_advisories: int = Field(description="Total number of advisories"),
+    high_severity_count: int = Field(description="Number of high severity advisories"),
+    medium_severity_count: int = Field(description="Number of medium severity advisories"),
+    low_severity_count: int = Field(description="Number of low severity advisories"),
+    summary_notes: str = Field(description="Notes for the advisory summary", default=""),
+):
+    """Store GHSA summary statistics for a repository."""
+    return backend.store_new_ghsa_summary(
+        process_repo(owner, repo),
+        total_advisories,
+        high_severity_count,
+        medium_severity_count,
+        low_severity_count,
+        summary_notes,
+    )
+
+
+@mcp.tool()
+def update_ghsa_summary_notes(
+    owner: str = Field(description="The owner of the GitHub repository"),
+    repo: str = Field(description="The name of the GitHub repository"),
+    summary_notes: str = Field(description="New notes for the advisory summary", default=""),
+):
+    """Update summary notes for the GHSA summary for a repository."""
+    repo_name = process_repo(owner, repo)
+    existing = backend.get_ghsa_summary(repo_name)
+    if not existing:
+        return f"Error: No GHSA summary exists in repo: {repo_name}"
+    return backend.store_new_ghsa_summary(
+        repo_name,
+        existing["total_advisories"],
+        existing["high_severity_count"],
+        existing["medium_severity_count"],
+        existing["low_severity_count"],
+        summary_notes,
+    )
+
+
+@mcp.tool()
+def get_ghsa_summary(
+    owner: str = Field(description="The owner of the GitHub repository"),
+    repo: str = Field(description="The name of the GitHub repository"),
+):
+    """Get the GHSA summary for a repository."""
+    repo_name = process_repo(owner, repo)
+    result = backend.get_ghsa_summary(repo_name)
+    if not result:
+        return f"Error: No GHSA summary exists in repo: {repo_name}"
+    return json.dumps(result)
+
+
+@mcp.tool()
+def clear_repo(
+    owner: str = Field(description="The owner of the GitHub repository"),
+    repo: str = Field(description="The name of the GitHub repository"),
+):
+    """Clear GHSA and GHSA summary records for a repository."""
+    return backend.clear_repo(process_repo(owner, repo))
+
 
 async def fetch_GHSA_details_from_gh(owner: str, repo: str, ghsa_id: str) -> str | dict:
     """Fetch the details of a repository security advisory."""

src/seclab_taskflows/mcp_servers/ghsa_models.py

@@ -0,0 +1,48 @@
+# SPDX-FileCopyrightText: GitHub, Inc.
+# SPDX-License-Identifier: MIT
+
+from sqlalchemy import Text
+from sqlalchemy.orm import DeclarativeBase, mapped_column, Mapped
+from typing import Optional
+
+
+class Base(DeclarativeBase):
+    pass
+
+class GHSA(Base):
+    __tablename__ = "ghsa"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    ghsa_id: Mapped[str]
+    repo: Mapped[str]
+    severity: Mapped[str]
+    cve_id: Mapped[Optional[str]] = mapped_column(nullable=True)
+    description: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    summary: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+    published_at: Mapped[Optional[str]] = mapped_column(nullable=True)
+    state: Mapped[Optional[str]] = mapped_column(nullable=True)
+
+    def __repr__(self):
+        return (
+            f"<GHSA(id={self.id}, ghsa_id={self.ghsa_id}, repo={self.repo}, "
+            f"severity={self.severity}, cve_id={self.cve_id}, description={self.description}, summary={self.summary}, "
+            f"published_at={self.published_at}, state={self.state})>"
+        )
+
+class GHSASummary(Base):
+    __tablename__ = "ghsa_summary"
+
+    id: Mapped[int] = mapped_column(primary_key=True)
+    repo: Mapped[str]
+    total_advisories: Mapped[int]
+    high_severity_count: Mapped[int]
+    medium_severity_count: Mapped[int]
+    low_severity_count: Mapped[int]
+    summary_notes: Mapped[Optional[str]] = mapped_column(Text, nullable=True)
+
+    def __repr__(self):
+        return (
+            f"<GHSASummary(id={self.id}, repo={self.repo}, total_advisories={self.total_advisories}, "
+            f"high_severity_count={self.high_severity_count}, medium_severity_count={self.medium_severity_count}, "
+            f"low_severity_count={self.low_severity_count}, summary_notes={self.summary_notes})>"
+        )

src/seclab_taskflows/prompts/audit/known_security_advisories.yaml

@@ -7,5 +7,8 @@ seclab-taskflow-agent:
 prompt: |
         ## Known Security Advisories for this Repository
 
-        Fetch the security advisories for {{ globals.repo }} from memcache (stored under the key 'security_advisories_{{ globals.repo }}'). If the value in the memcache is null or an error message, clearly state that no advisories are available and skip advisory analysis. Otherwise, state how many advisories were found.
+        Fetch the security advisories for {{ globals.repo }} from the GHSASummary and GHSA entries 
+        stored in the database. Do not fetch them from GitHub directly.
+        If the value in the database is null or an error message, clearly state that no advisories are available and skip advisory analysis. 
+        Otherwise, state how many advisories were found.
         Review these advisories and consider them when identifying security risks. If you identify code that is similar to a known advisory pattern, highlight that connection.

src/seclab_taskflows/taskflows/audit/audit_issue_local_iter.yaml

@@ -50,4 +50,4 @@ taskflow:
       toolboxes:
         - seclab_taskflows.toolboxes.repo_context
         - seclab_taskflows.toolboxes.local_file_viewer
-        - seclab_taskflow_agent.toolboxes.memcache
+        - seclab_taskflows.toolboxes.ghsa

src/seclab_taskflows/taskflows/audit/classify_application_local.yaml

@@ -90,4 +90,4 @@ taskflow:
       toolboxes:
         - seclab_taskflows.toolboxes.repo_context
         - seclab_taskflows.toolboxes.local_file_viewer
-        - seclab_taskflow_agent.toolboxes.memcache
+        - seclab_taskflows.toolboxes.ghsa