Feature/merge dev to main (#962)

* merge dev and main

* git rm

* add back collection fix

py/cli/commands/server.py

@@ -217,7 +217,7 @@ def serve(
             ).replace(":", "")
 
     if docker:
-        
+
         run_docker_serve(
             client,
             host,

py/cli/utils/docker_utils.py

@@ -377,7 +377,7 @@ def build_docker_command(
     os.environ["TRAEFIK_PORT"] = str(available_port + 1)
 
     os.environ["CONFIG_PATH"] = (
-        os.path.basename(config_path) if config_path else ""
+        os.path.abspath(config_path) if config_path else ""
     )
 
     os.environ["R2R_IMAGE"] = image or ""

py/core/base/abstractions/__init__.py

@@ -31,8 +31,8 @@
 from .restructure import KGEnrichmentSettings
 from .search import (
     AggregateSearchResult,
-    KGLocalSearchResult,
     KGGlobalSearchResult,
+    KGLocalSearchResult,
     KGSearchResult,
     KGSearchSettings,
     VectorSearchResult,

py/core/base/abstractions/search.py

@@ -54,8 +54,10 @@ class Config:
             },
         }
 
+
 class KGLocalSearchResult(BaseModel):
     """Result of a local knowledge graph search operation."""
+
     query: str
     entities: dict[str, Any]
     relationships: dict[str, Any]
@@ -70,6 +72,7 @@ def __repr__(self) -> str:
 
 class KGGlobalSearchResult(BaseModel):
     """Result of a global knowledge graph search operation."""
+
     query: str
     search_result: list[str]
 
@@ -80,26 +83,29 @@ def __repr__(self) -> str:
         return self.__str__()
 
     def dict(self) -> dict:
-        return {
-            "query": self.query,
-            "search_result": self.search_result
-        }
+        return {"query": self.query, "search_result": self.search_result}
+
 
 class KGSearchResult(BaseModel):
     """Result of a knowledge graph search operation."""
+
     local_result: Optional[KGLocalSearchResult] = None
     global_result: Optional[KGGlobalSearchResult] = None
-    
+
     def __str__(self) -> str:
         return f"KGSearchResult(local_result={self.local_result}, global_result={self.global_result})"
 
     def __repr__(self) -> str:
         return self.__str__()
-    
+
     def dict(self) -> dict:
         return {
-            "local_result": self.local_result.dict() if self.local_result else None,
-            "global_result": self.global_result.dict() if self.global_result else None
+            "local_result": (
+                self.local_result.dict() if self.local_result else None
+            ),
+            "global_result": (
+                self.global_result.dict() if self.global_result else None
+            ),
         }
 
 

py/core/base/providers/auth.py

@@ -82,7 +82,9 @@ def register(self, email: str, password: str) -> Dict[str, str]:
         pass
 
     @abstractmethod
-    def verify_email(self, email: str, verification_code: str) -> Dict[str, str]:
+    def verify_email(
+        self, email: str, verification_code: str
+    ) -> Dict[str, str]:
         pass
 
     @abstractmethod

py/core/main/api/routes/auth/base.py

@@ -48,7 +48,7 @@ async def verify_email_app(
             email: EmailStr = Body(..., description="User's email address"),
             verification_code: str = Body(
                 ..., description="Email verification code"
-            )
+            ),
         ):
             """
             Verify a user's email address.

py/core/main/api/routes/retrieval/base.py

@@ -62,7 +62,7 @@ async def search_app(
                 description=search_descriptions.get("kg_search_settings"),
             ),
             auth_user=Depends(self.engine.providers.auth.auth_wrapper),
-        )  -> WrappedSearchResponse:
+        ) -> WrappedSearchResponse:
             """
             Perform a search query on the vector database and knowledge graph.
 

py/core/main/assembly/config.py

@@ -1,7 +1,8 @@
 import logging
 import os
 from enum import Enum
-from typing import Any
+from pathlib import Path
+from typing import Any, Optional
 
 import toml
 from pydantic import BaseModel
@@ -58,7 +59,13 @@ class R2RConfig:
     prompt: PromptConfig
     agent: AgentConfig
 
-    def __init__(self, config_data: dict[str, Any]):
+    def __init__(
+        self, config_data: dict[str, Any], base_path: Optional[Path] = None
+    ):
+        """
+        :param config_data: dictionary of configuration parameters
+        :param base_path: base path when a relative path is specified for the prompts directory
+        """
         # Load the default configuration
         default_config = self.load_default_config()
 
@@ -79,6 +86,18 @@ def __init__(self, config_data: dict[str, Any]):
                 and default_config[section]["provider"] != "null"
             ):
                 self._validate_config_section(default_config, section, keys)
+                if (
+                    section == "prompt"
+                    and "file_path" in default_config[section]
+                    and not Path(
+                        default_config[section]["file_path"]
+                    ).is_absolute()
+                    and base_path
+                ):
+                    # Make file_path absolute and relative to the base path
+                    default_config[section]["file_path"] = str(
+                        base_path / default_config[section]["file_path"]
+                    )
             setattr(self, section, default_config[section])
         self.completion = CompletionConfig.create(**self.completion)
         # override GenerationConfig defaults
@@ -122,7 +141,7 @@ def from_toml(cls, config_path: str = None) -> "R2RConfig":
         with open(config_path) as f:
             config_data = toml.load(f)
 
-        return cls(config_data)
+        return cls(config_data, base_path=Path(config_path).parent)
 
     def to_toml(self):
         config_data = {

py/core/main/services/auth_service.py

@@ -49,7 +49,7 @@ async def verify_email(self, email: str, verification_code: str) -> bool:
             raise R2RException(
                 status_code=400, message="Invalid or expired verification code"
             )
-        
+
         user = self.providers.database.relational.get_user_by_id(user_id)
         if not user or user.email != email:
             raise R2RException(

py/core/parsers/structured/csv_parser.py

@@ -1,4 +1,4 @@
-from typing import IO, AsyncGenerator, Union
+from typing import IO, AsyncGenerator, Optional, Union
 
 from core.base.abstractions.document import DataType
 from core.base.parsers.base_parser import AsyncParser
@@ -36,7 +36,7 @@ def __init__(self):
         self.StringIO = StringIO
 
     def get_delimiter(
-        self, file_path: str | None = None, file: IO[bytes] | None = None
+        self, file_path: Optional[str] = None, file: Optional[IO[bytes]] = None
     ):
 
         sniffer = self.csv.Sniffer()

py/core/pipes/retrieval/kg_search_search_pipe.py

@@ -12,8 +12,8 @@
     KGSearchSettings,
     PipeType,
     PromptProvider,
+    R2RException,
     RunLoggingSingleton,
-    R2RException
 )
 from core.base.abstractions.search import (
     KGGlobalSearchResult,
@@ -25,6 +25,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 class KGSearchSearchPipe(GeneratorPipe):
     """
     Embeds and stores documents using a specified embedding model and database.
@@ -132,11 +133,18 @@ async def local_search(
                 )
                 all_search_results.append(search_result)
 
-
-            if len(all_search_results[0])==0:
-                raise R2RException("No search results found. Please make sure you have run the KG enrichment step before running the search: r2r enrich-graph", 400)
+            if len(all_search_results[0]) == 0:
+                raise R2RException(
+                    "No search results found. Please make sure you have run the KG enrichment step before running the search: r2r enrich-graph",
+                    400,
+                )
 
-            yield KGLocalSearchResult(query=message, entities=all_search_results[0], relationships=all_search_results[1], communities=all_search_results[2])
+            yield KGLocalSearchResult(
+                query=message,
+                entities=all_search_results[0],
+                relationships=all_search_results[1],
+                communities=all_search_results[2],
+            )
 
     async def global_search(
         self,

py/core/providers/database/postgres.py

@@ -70,7 +70,7 @@ def __init__(
         ) or os.getenv("POSTGRES_VECS_COLLECTION")
         if not collection_name:
             raise ValueError(
-                "Error, please set a valid POSTGRES_VECS_COLLECTION environment variable or set a 'collection' in the 'database' settings of your `r2r.toml`."
+                "Error, please set a valid POSTGRES_VECS_COLLECTION environment variable or set a 'vecs_collection' in the 'database' settings of your `r2r.toml`."
             )
 
         if not all([user, password, host, port, db_name, collection_name]):

py/core/providers/database/vecs/collection.py

@@ -378,7 +378,7 @@ def _create(self):
                 tsvector_update_trigger(fts, 'pg_catalog.english', text);
             """
                 )
-        )
+            )
         return self
 
     def _drop(self):
@@ -1174,6 +1174,8 @@ def _build_table(name: str, meta: MetaData, dimension: int) -> Table:
         table.c.fts,
         table.c.text,
         postgresql_using="gin",
-        postgresql_ops={"text": "gin_trgm_ops"},  # alternative,  gin_tsvector_ops
+        postgresql_ops={
+            "text": "gin_trgm_ops"
+        },  # alternative,  gin_tsvector_ops
     )
     return table

py/core/providers/database/vector.py

@@ -131,7 +131,7 @@ def _initialize_vector_db(self, dimension: int) -> None:
         self.collection = self.vx.get_or_create_collection(
             name=self.collection_name, dimension=dimension
         )
-        
+
     def upsert(self, entry: VectorEntry) -> None:
         if self.collection is None:
             raise ValueError(

py/sdk/models.py

@@ -187,6 +187,7 @@ class Config:
             },
         }
 
+
 class KGLocalSearchResult(BaseModel):
     query: str
     entities: list[dict[str, Any]]
@@ -195,15 +196,16 @@ class KGLocalSearchResult(BaseModel):
 
     def __str__(self) -> str:
         return f"KGLocalSearchResult(query={self.query}, entities={self.entities}, relationships={self.relationships}, communities={self.communities})"
-    
+
     def dict(self) -> dict:
         return {
             "query": self.query,
             "entities": self.entities,
             "relationships": self.relationships,
-            "communities": self.communities
+            "communities": self.communities,
         }
 
+
 class KGGlobalSearchResult(BaseModel):
     query: str
     search_result: list[str]
@@ -213,12 +215,9 @@ def __str__(self) -> str:
 
     def __repr__(self) -> str:
         return self.__str__()
-    
+
     def dict(self) -> dict:
-        return {
-            "query": self.query,
-            "search_result": self.search_result
-        }
+        return {"query": self.query, "search_result": self.search_result}
 
 
 class KGSearchResult(BaseModel):
@@ -230,11 +229,15 @@ def __str__(self) -> str:
 
     def __repr__(self) -> str:
         return self.__str__()
-    
+
     def dict(self) -> dict:
         return {
-            "local_result": self.local_result.dict() if self.local_result else None,
-            "global_result": self.global_result.dict() if self.global_result else None
+            "local_result": (
+                self.local_result.dict() if self.local_result else None
+            ),
+            "global_result": (
+                self.global_result.dict() if self.global_result else None
+            ),
         }
 
     class Config:
@@ -245,7 +248,7 @@ class Config:
                     "entities": {
                         "Paris": {
                             "name": "Paris",
-                            "description": "Paris is the capital of France."
+                            "description": "Paris is the capital of France.",
                         }
                     },
                     "relationships": {},
@@ -255,11 +258,12 @@ class Config:
                     "query": "What is the capital of France?",
                     "search_result": [
                         "Paris is the capital and most populous city of France."
-                    ]
-                }
+                    ],
+                },
             }
         }
 
+
 class R2RException(Exception):
     def __init__(
         self, message: str, status_code: int, detail: Optional[Any] = None