Upload folder using huggingface_hub

document_qa/document_qa_engine.py

@@ -34,7 +34,7 @@ class TextMerger:
 
     Args:
         model_name: A tiktoken model name (e.g. ``"gpt-4"``).  When given,
-            the tokenizer for that model is used.  
+            the tokenizer for that model is used.
         encoding_name: A tiktoken encoding name (default ``"gpt2"``).
             Ignored when *model_name* is provided.
     """
@@ -174,7 +174,7 @@ class DataStorage:
 
     Args:
         embedding_function: A LangChain-compatible ``Embeddings`` instance
-        root_path: Optional directory for persisted embeddings. 
+        root_path: Optional directory for persisted embeddings.
         engine: The vector-store class to use.
 
     """
@@ -278,7 +278,7 @@ class DocumentQAEngine:
     Args:
         llm: A LangChain chat model (e.g. ``ChatOpenAI``).
         data_storage: A `DataStorage` instance for managing embeddings.
-        grobid_url: URL of the GROBID server. 
+        grobid_url: URL of the GROBID server.
         memory: Optional ``ConversationBufferMemory`` for multi-turn context.
 
     """
@@ -297,7 +297,8 @@ class DocumentQAEngine:
                  llm,
                  data_storage: DataStorage,
                  grobid_url=None,
-                 memory=None
+                 memory=None,
+                 ping_grobid_server: bool = True
                  ):
 
         self.llm = llm
@@ -307,7 +308,7 @@ class DocumentQAEngine:
         self.data_storage = data_storage
 
         if grobid_url:
-            self.grobid_processor = GrobidProcessor(grobid_url)
+            self.grobid_processor = GrobidProcessor(grobid_url, ping_server=ping_grobid_server)
 
     def query_document(
             self,
@@ -317,7 +318,7 @@ class DocumentQAEngine:
             context_size=4,
             extraction_schema=None,
             verbose=False
-    ) -> tuple[Any, str]:
+    ) -> tuple[Any, str, list]:
         """Ask a question and get an LLM-generated answer.
 
         Retrieves the most relevant chunks from the vector store, feeds
@@ -354,7 +355,7 @@ class DocumentQAEngine:
 
         if output_parser:
             try:
-                return self._parse_json(response, output_parser), response
+                return self._parse_json(response, output_parser), response, coordinates
             except Exception as oe:
                 print("Failing to parse the response", oe)
                 return None, response, coordinates
@@ -369,7 +370,7 @@ class DocumentQAEngine:
         else:
             return None, response, coordinates
 
-    def query_storage(self, query: str, doc_id, context_size=4) -> tuple[List[Document], list]:
+    def query_storage(self, query: str, doc_id, context_size=4) -> tuple[List[str], list]:
         """Retrieve relevant text passages without calling the LLM.
 
         Useful for debugging which chunks would be used as context, or for
@@ -480,7 +481,7 @@ class DocumentQAEngine:
 
         return parsed_output
 
-    def _run_query(self, doc_id, query, context_size=4) -> tuple[List[Document], list]:
+    def _run_query(self, doc_id, query, context_size=4) -> tuple[Any, list]:
         relevant_documents, relevant_document_coordinates = self._get_context(doc_id, query, context_size)
         response = self.chain.invoke({"context": relevant_documents, "question": query})
         return response, relevant_document_coordinates
@@ -550,7 +551,7 @@ class DocumentQAEngine:
         biblio['filename'] = filename.replace(" ", "_")
 
         if verbose:
-            print("Generating embeddings for:", hash, ", filename: ", filename)
+            print("Generating embeddings for filename: ", filename)
 
         texts = []
         metadatas = []

document_qa/grobid_processors.py

@@ -20,10 +20,19 @@ from pathlib import Path
 
 import dateparser
 import grobid_tei_xml
+import requests
 from bs4 import BeautifulSoup
 from grobid_client.grobid_client import GrobidClient
 
 
+class GrobidServiceError(RuntimeError):
+    """Raised when the Grobid service fails to process a document."""
+
+    def __init__(self, message="Grobid service error", status_code=None):
+        super().__init__(message)
+        self.status_code = status_code
+
+
 def get_span_start(type, title=None):
     """Return an opening ``<span>`` tag for an annotation of the given *type*."""
     title_ = ' title="' + title + '"' if title is not None else ""
@@ -168,22 +177,57 @@ class GrobidProcessor(BaseProcessor):
 
             Returns ``None`` if GROBID returns a non-200 status.
         """
-        pdf_file, status, text = self.grobid_client.process_pdf("processFulltextDocument",
-                                                                input_path,
-                                                                consolidate_header=True,
-                                                                consolidate_citations=False,
-                                                                segment_sentences=False,
-                                                                tei_coordinates=coordinates,
-                                                                include_raw_citations=False,
-                                                                include_raw_affiliations=False,
-                                                                generateIDs=True)
+        try:
+            pdf_file, status, text = self.grobid_client.process_pdf("processFulltextDocument",
+                                                                    input_path,
+                                                                    consolidate_header=True,
+                                                                    consolidate_citations=False,
+                                                                    segment_sentences=False,
+                                                                    tei_coordinates=coordinates,
+                                                                    include_raw_citations=False,
+                                                                    include_raw_affiliations=False,
+                                                                    generateIDs=True)
+        except requests.exceptions.RequestException as exc:
+            # Transport-level failure (connection refused, timeout, …).
+            # Local/usage errors (bad path, parsing bugs) are intentionally
+            # not caught here so they surface with their real traceback.
+            raise GrobidServiceError("Grobid service did not respond.") from exc
 
         if status != 200:
-            return
+            raise GrobidServiceError(
+                f"Grobid service returned status {status}.",
+                status_code=status
+            )
+
+        # Grobid can answer 200 with an empty body (e.g. it gave up on the PDF).
+        if not text or not text.strip():
+            raise GrobidServiceError(
+                "Grobid returned an empty response.",
+                status_code=status
+            )
+
+        # A truncated/corrupted TEI payload makes the XML parser blow up; map
+        # that to a clear service error instead of an opaque parsing traceback.
+        try:
+            document_object = self.parse_grobid_xml(text, coordinates=coordinates)
+        except GrobidServiceError:
+            raise
+        except Exception as exc:
+            raise GrobidServiceError(
+                "Grobid returned a malformed or truncated response.",
+                status_code=status
+            ) from exc
 
-        document_object = self.parse_grobid_xml(text, coordinates=coordinates)
         document_object['filename'] = Path(pdf_file).stem.replace(".tei", "")
 
+        # Well-formed XML can still carry no usable text (e.g. an image-only or
+        # truncated PDF). Nothing to embed downstream, so fail loudly here.
+        if not any(passage.get('text', '').strip() for passage in document_object.get('passages', [])):
+            raise GrobidServiceError(
+                "Grobid returned a document with no extractable text.",
+                status_code=status
+            )
+
         return document_object
 
     def process_single(self, input_file):
@@ -221,7 +265,7 @@ class GrobidProcessor(BaseProcessor):
         try:
             year = dateparser.parse(doc_biblio.header.date).year
             biblio["publication_year"] = year
-        except:
+        except Exception:
             pass
 
         output_data['biblio'] = biblio

requirements.txt

@@ -1,6 +1,6 @@
 # Grobid
 grobid-quantities-client==0.4.0
-grobid-client-python==0.0.9
+grobid-client-python==0.1.4
 grobid-tei-xml==0.1.3
 
 # Utils
@@ -30,6 +30,6 @@ typing-inspect==0.9.0
 typing_extensions==4.12.2
 pydantic==2.10.6
 sentence-transformers==2.6.1
-streamlit-pdf-viewer==0.0.25
+streamlit-pdf-viewer==0.0.29
 umap-learn==0.5.6
 plotly==5.20.0

streamlit_app.py

@@ -15,20 +15,19 @@ from hashlib import blake2b
 from tempfile import NamedTemporaryFile
 
 import dotenv
+import streamlit as st
 from grobid_quantities.quantities import QuantitiesAPI
 from langchain.memory import ConversationBufferMemory
 from langchain_openai import ChatOpenAI
 from streamlit_pdf_viewer import pdf_viewer
 
 from document_qa.custom_embeddings import ModalEmbeddings
+from document_qa.document_qa_engine import DocumentQAEngine, DataStorage
+from document_qa.grobid_processors import GrobidAggregationProcessor, decorate_text_with_annotations, GrobidServiceError
 from document_qa.ner_client_generic import NERClientGeneric
 
 dotenv.load_dotenv(override=True)
 
-import streamlit as st
-from document_qa.document_qa_engine import DocumentQAEngine, DataStorage
-from document_qa.grobid_processors import GrobidAggregationProcessor, decorate_text_with_annotations
-
 API_MODELS = {
     "microsoft/Phi-4-mini-instruct": os.environ["PHI_URL"],
     "Qwen/Qwen3-0.6B": os.environ["QWEN_URL"]
@@ -169,7 +168,13 @@ def init_qa(model_name, embeddings_name):
     )
 
     storage = DataStorage(embeddings)
-    return DocumentQAEngine(chat, storage, grobid_url=os.environ['GROBID_URL'], memory=st.session_state['memory'])
+    return DocumentQAEngine(
+        chat,
+        storage,
+        grobid_url=os.environ['GROBID_URL'],
+        memory=st.session_state['memory'],
+        ping_grobid_server=False
+    )
 
 
 @st.cache_resource
@@ -358,19 +363,36 @@ if uploaded_file and not st.session_state.loaded_embeddings:
         st.stop()
 
     with left_column:
-        with st.spinner('Reading file, calling Grobid, and creating in-memory embeddings...'):
-            binary = uploaded_file.getvalue()
-            tmp_file = NamedTemporaryFile()
-            tmp_file.write(bytearray(binary))
-            st.session_state['binary'] = binary
-
-            st.session_state['doc_id'] = hash = st.session_state['rqa'][model].create_memory_embeddings(
-                tmp_file.name,
-                chunk_size=chunk_size,
-                perc_overlap=0.1
-            )
-            st.session_state['loaded_embeddings'] = True
-            st.session_state.messages = []
+        try:
+            with st.spinner('Reading file, calling Grobid, and creating in-memory embeddings...'):
+                binary = uploaded_file.getvalue()
+                tmp_path = None
+                try:
+                    with NamedTemporaryFile(suffix=".pdf", delete=False) as tmp_file:
+                        tmp_file.write(bytearray(binary))
+                        tmp_file.flush()
+                        tmp_path = tmp_file.name
+                    st.session_state['binary'] = binary
+
+                    st.session_state['doc_id'] = st.session_state['rqa'][model].create_memory_embeddings(
+                        tmp_path,
+                        chunk_size=chunk_size,
+                        perc_overlap=0.1
+                    )
+                finally:
+                    if tmp_path and os.path.exists(tmp_path):
+                        os.unlink(tmp_path)
+                st.session_state['loaded_embeddings'] = True
+                st.session_state.messages = []
+        except GrobidServiceError as exc:
+            st.session_state['doc_id'] = None
+            st.session_state['loaded_embeddings'] = False
+            st.session_state['uploaded'] = False
+            message = str(exc).strip() or "Grobid is not responding."
+            if not message.endswith((".", "!", "?")):
+                message += "."
+            st.error(f"{message} Please try again later.")
+            st.stop()
 
 
 def rgb_to_hex(rgb):