feat(research): close citation graph and obsidian export gaps

config/config.yaml

@@ -126,3 +126,5 @@ obsidian:
   auto_export_on_save: true
   auto_sync_tracks: true
   export_limit: 200
+  track_moc_filename: "_MOC.md"
+  group_tracks_in_folders: true

config/settings.py

@@ -142,6 +142,8 @@ class ObsidianConfig(BaseModel):
     auto_export_on_save: bool = True
     auto_sync_tracks: bool = True
     export_limit: int = 200
+    track_moc_filename: str = "_MOC.md"
+    group_tracks_in_folders: bool = True
 
 
 class CollabHostConfig(BaseModel):
@@ -334,6 +336,8 @@ def load_environment_variables(self) -> None:
         obsidian_auto_export = os.getenv("PAPERBOT_OBSIDIAN_AUTO_EXPORT")
         obsidian_auto_sync_tracks = os.getenv("PAPERBOT_OBSIDIAN_AUTO_SYNC_TRACKS")
         obsidian_export_limit = os.getenv("PAPERBOT_OBSIDIAN_EXPORT_LIMIT")
+        obsidian_track_moc_filename = os.getenv("PAPERBOT_OBSIDIAN_TRACK_MOC_FILENAME")
+        obsidian_group_tracks = os.getenv("PAPERBOT_OBSIDIAN_GROUP_TRACKS_IN_FOLDERS")
         if re_enabled is not None:
             self.report_engine.enabled = re_enabled.lower() in ("1", "true", "yes", "on")
         if re_api:
@@ -393,6 +397,15 @@ def load_environment_variables(self) -> None:
                     "Ignoring invalid PAPERBOT_OBSIDIAN_EXPORT_LIMIT=%r; expected an integer",
                     obsidian_export_limit,
                 )
+        if obsidian_track_moc_filename:
+            self.obsidian.track_moc_filename = obsidian_track_moc_filename
+        if obsidian_group_tracks is not None:
+            self.obsidian.group_tracks_in_folders = obsidian_group_tracks.lower() in (
+                "1",
+                "true",
+                "yes",
+                "on",
+            )
 
         # Collab host LLM
         host_api = os.getenv("PAPERBOT_HOST_API_KEY")

src/paperbot/api/main.py

@@ -24,6 +24,7 @@
     research,
     paperscool,
     newsletter,
+    obsidian,
     harvest,
     model_endpoints,
     studio_chat,
@@ -80,6 +81,7 @@ async def health_check():
 app.include_router(research.router, prefix="/api", tags=["Research"])
 app.include_router(paperscool.router, prefix="/api", tags=["PapersCool"])
 app.include_router(newsletter.router, prefix="/api", tags=["Newsletter"])
+app.include_router(obsidian.router, prefix="/api", tags=["Obsidian"])
 app.include_router(harvest.router, prefix="/api", tags=["Harvest"])
 app.include_router(model_endpoints.router, prefix="/api", tags=["Model Endpoints"])
 app.include_router(studio_chat.router, prefix="/api", tags=["Studio Chat"])

src/paperbot/api/routes/__init__.py

@@ -14,6 +14,7 @@
     research,
     paperscool,
     newsletter,
+    obsidian,
     model_endpoints,
     repro_context,
     feed,
@@ -36,6 +37,7 @@
     "research",
     "paperscool",
     "newsletter",
+    "obsidian",
     "model_endpoints",
     "repro_context",
     "feed",

src/paperbot/api/routes/obsidian.py

@@ -0,0 +1,86 @@
+from __future__ import annotations
+
+from pathlib import Path
+from typing import List, Optional
+
+from fastapi import APIRouter, HTTPException
+from pydantic import BaseModel, Field
+
+from config.settings import create_settings
+from paperbot.infrastructure.exporters import ObsidianReportExporter
+
+router = APIRouter()
+
+
+class ObsidianReportCitationRequest(BaseModel):
+    title: str = Field(..., min_length=1, max_length=500)
+    year: Optional[int] = None
+    authors: List[str] = Field(default_factory=list)
+    relevant_finding: str = ""
+    doi: Optional[str] = None
+    arxiv_id: Optional[str] = None
+    semantic_scholar_id: Optional[str] = None
+    id: Optional[str] = None
+
+
+class ObsidianReportSectionRequest(BaseModel):
+    title: str = Field(..., min_length=1, max_length=200)
+    content: str = ""
+    cited_papers: List[ObsidianReportCitationRequest] = Field(default_factory=list)
+
+
+class ObsidianMethodComparisonRequest(BaseModel):
+    name: str = Field(..., min_length=1, max_length=120)
+    paper: str = Field(..., min_length=1, max_length=500)
+    pros: str = ""
+    cons: str = ""
+
+
+class ObsidianExportReportRequest(BaseModel):
+    title: str = Field(..., min_length=1, max_length=300)
+    vault_path: Optional[str] = None
+    root_dir: Optional[str] = None
+    track_name: Optional[str] = Field(default=None, max_length=128)
+    workflow_type: str = "research"
+    summary: str = ""
+    key_insight: str = ""
+    sections: List[ObsidianReportSectionRequest] = Field(default_factory=list)
+    methods: List[ObsidianMethodComparisonRequest] = Field(default_factory=list)
+    trends: str = ""
+    future_directions: str = ""
+    references: List[ObsidianReportCitationRequest] = Field(default_factory=list)
+    tags: List[str] = Field(default_factory=list)
+
+
+class ObsidianExportReportResponse(BaseModel):
+    vault_path: str
+    root_dir: str
+    title: str
+    note_path: str
+
+
+@router.post("/obsidian/export-report", response_model=ObsidianExportReportResponse)
+def export_obsidian_report(req: ObsidianExportReportRequest) -> ObsidianExportReportResponse:
+    settings = create_settings()
+    obsidian_config = settings.obsidian
+
+    vault_value = str(req.vault_path or obsidian_config.vault_path or "").strip()
+    if not vault_value:
+        raise HTTPException(
+            status_code=400,
+            detail="vault_path is required. Pass it in the request or configure obsidian.vault_path.",
+        )
+
+    exporter = ObsidianReportExporter()
+    try:
+        result = exporter.export_report_note(
+            vault_path=Path(vault_value),
+            report=req.model_dump(),
+            root_dir=str(req.root_dir or obsidian_config.root_dir or "PaperBot"),
+            track_moc_filename=getattr(obsidian_config, "track_moc_filename", "_MOC.md"),
+            group_tracks_in_folders=getattr(obsidian_config, "group_tracks_in_folders", True),
+        )
+    except ValueError as exc:
+        raise HTTPException(status_code=400, detail=str(exc)) from exc
+
+    return ObsidianExportReportResponse(**result)

src/paperbot/application/ports/vault_exporter_port.py

@@ -18,4 +18,6 @@ def export_library_snapshot(
         track: Optional[Dict[str, Any]] = None,
         root_dir: str = "PaperBot",
         paper_template_path: Optional[Path] = None,
+        track_moc_filename: str = "_MOC.md",
+        group_tracks_in_folders: bool = True,
     ) -> Dict[str, Any]: ...

src/paperbot/infrastructure/api_clients/__init__.py

@@ -3,12 +3,17 @@
 """
 
 from .base import APIClient
+from .citation_graph import CitationGraph, CitationGraphClient, CitationGraphEdge, CitationGraphNode
 from .github_client import GitHubRadarClient
 from .semantic_scholar import SemanticScholarClient
 from .x_client import XRecentSearchClient
 
 __all__ = [
     "APIClient",
+    "CitationGraph",
+    "CitationGraphClient",
+    "CitationGraphEdge",
+    "CitationGraphNode",
     "GitHubRadarClient",
     "SemanticScholarClient",
     "XRecentSearchClient",