update dockerfile to address glibcxx issue (#468)

Co-authored-by: Jeremy Dyer <[email protected]>

Dockerfile

@@ -4,7 +4,7 @@
 # syntax=docker/dockerfile:1.3
 
 ARG BASE_IMG=nvcr.io/nvidia/cuda
-ARG BASE_IMG_TAG=12.4.1-base-ubuntu22.04
+ARG BASE_IMG_TAG=12.5.1-base-ubuntu22.04
 
 # Use NVIDIA Morpheus as the base image
 FROM $BASE_IMG:$BASE_IMG_TAG AS base
@@ -21,13 +21,20 @@ LABEL git_commit=$GIT_COMMIT
 
 # Install necessary dependencies using apt-get
 RUN apt-get update && apt-get install -y \
-      wget \
       bzip2 \
       ca-certificates \
       curl \
       libgl1-mesa-glx \
+      software-properties-common \
+      wget \
     && apt-get clean
 
+# A workaround for the error (mrc-core): /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.32' not found
+# Issue: https://github.com/NVIDIA/nv-ingest/issues/474
+RUN add-apt-repository -y ppa:ubuntu-toolchain-r/test \
+    && apt-get update \
+    && apt-get install -y --only-upgrade libstdc++6
+
 RUN wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O /tmp/miniforge.sh \
     && bash /tmp/miniforge.sh -b -p /opt/conda \
     && rm /tmp/miniforge.sh

src/nv_ingest/extraction_workflows/pdf/nemoretriever_parse_helper.py

@@ -96,9 +96,6 @@ def nemoretriever_parse(
     """
     logger.debug("Extracting PDF with nemoretriever_parse backend.")
 
-    nemoretriever_parse_config = kwargs.get("nemoretriever_parse_config", {})
-    nemoretriever_parse_config = nemoretriever_parse_config if nemoretriever_parse_config is not None else {}
-
     row_data = kwargs.get("row_data")
     # get source_id
     source_id = row_data["source_id"]
@@ -111,9 +108,10 @@ def nemoretriever_parse(
     paddle_output_format = kwargs.get("paddle_output_format", "pseudo_markdown")
     paddle_output_format = TableFormatEnum[paddle_output_format.upper()]
 
-    pdfium_config = kwargs.get("pdfium_config", {})
-    if isinstance(pdfium_config, dict):
-        pdfium_config = PDFiumConfigSchema(**pdfium_config)
+    if (extract_tables_method == "yolox") and (extract_tables or extract_charts):
+        pdfium_config = kwargs.get("pdfium_config", {})
+        if isinstance(pdfium_config, dict):
+            pdfium_config = PDFiumConfigSchema(**pdfium_config)
     nemoretriever_parse_config = kwargs.get("nemoretriever_parse_config", {})
     if isinstance(nemoretriever_parse_config, dict):
         nemoretriever_parse_config = NemoRetrieverParseConfigSchema(**nemoretriever_parse_config)

src/nv_ingest/schemas/pdf_extractor_schema.py

@@ -73,7 +73,7 @@ def validate_endpoints(cls, values):
 
         for model_name in ["yolox"]:
             endpoint_name = f"{model_name}_endpoints"
-            grpc_service, http_service = values.get(endpoint_name)
+            grpc_service, http_service = values.get(endpoint_name, ("", ""))
             grpc_service = _clean_service(grpc_service)
             http_service = _clean_service(http_service)
 
@@ -156,7 +156,7 @@ def validate_endpoints(cls, values):
 
         for model_name in ["nemoretriever_parse"]:
             endpoint_name = f"{model_name}_endpoints"
-            grpc_service, http_service = values.get(endpoint_name)
+            grpc_service, http_service = values.get(endpoint_name, ("", ""))
             grpc_service = _clean_service(grpc_service)
             http_service = _clean_service(http_service)
 

src/nv_ingest/stages/nim/chart_extraction.py

@@ -66,9 +66,6 @@ def _update_metadata(
             # Image is too small; mark as skipped.
             results[i] = (img, None)
 
-    if not valid_images:
-        return results
-
     # Prepare data payloads for both clients.
     data_yolox = {"images": valid_arrays}
     data_paddle = {"base64_images": valid_images}

src/nv_ingest/stages/nim/table_extraction.py

@@ -54,7 +54,7 @@ def _update_metadata(
     logger.debug(f"Running table extraction using protocol {paddle_client.protocol}")
 
     # Initialize the results list in the same order as base64_images.
-    results: List[Optional[Tuple[str, Tuple[Any, Any, Any]]]] = ["", (None, None, None)] * len(base64_images)
+    results: List[Optional[Tuple[str, Tuple[Any, Any, Any]]]] = [("", None, None, None)] * len(base64_images)
 
     valid_images: List[str] = []
     valid_indices: List[int] = []
@@ -70,7 +70,7 @@ def _update_metadata(
             valid_indices.append(i)
         else:
             # Image is too small; mark as skipped.
-            results[i] = ("", None, None, None)
+            results[i] = (img, None, None, None)
 
     if not valid_images:
         return results

tests/nv_ingest/extraction_workflows/pdf/test_nemoretriever_parse_helper.py

@@ -34,26 +34,37 @@ def sample_pdf_stream():
     return pdf_stream
 
 
+@pytest.fixture
+def mock_parser_config():
+    return {
+        "nemoretriever_parse_endpoints": ("parser:8001", "http://parser:8000"),
+    }
+
+
 @patch(f"{_MODULE_UNDER_TEST}.create_inference_client")
-def test_nemoretriever_parse_text_extraction(mock_client, sample_pdf_stream, document_df):
+def test_nemoretriever_parse_text_extraction(mock_client, sample_pdf_stream, document_df, mock_parser_config):
     mock_client_instance = MagicMock()
     mock_client.return_value = mock_client_instance
     mock_client_instance.infer.return_value = [
-        {
-            "bbox": {"xmin": 0.16633729456384325, "ymin": 0.0969, "xmax": 0.3097820480404551, "ymax": 0.1102},
-            "text": "testing",
-            "type": "Text",
-        }
+        [
+            {
+                "bbox": {"xmin": 0.16633729456384325, "ymin": 0.0969, "xmax": 0.3097820480404551, "ymax": 0.1102},
+                "text": "testing",
+                "type": "Text",
+            }
+        ]
     ]
 
     result = nemoretriever_parse(
         pdf_stream=sample_pdf_stream,
         extract_text=True,
         extract_images=False,
         extract_tables=False,
+        extract_charts=False,
         row_data=document_df.iloc[0],
         text_depth="page",
-        nemoretriever_parse_config=MagicMock(),
+        extract_tables_method="nemoretriever_parse",
+        nemoretriever_parse_config=mock_parser_config,
     )
 
     assert len(result) == 1
@@ -63,25 +74,29 @@ def test_nemoretriever_parse_text_extraction(mock_client, sample_pdf_stream, doc
 
 
 @patch(f"{_MODULE_UNDER_TEST}.create_inference_client")
-def test_nemoretriever_parse_table_extraction(mock_client, sample_pdf_stream, document_df):
+def test_nemoretriever_parse_table_extraction(mock_client, sample_pdf_stream, document_df, mock_parser_config):
     mock_client_instance = MagicMock()
     mock_client.return_value = mock_client_instance
     mock_client_instance.infer.return_value = [
-        {
-            "bbox": {"xmin": 1 / 1024, "ymin": 2 / 1280, "xmax": 101 / 1024, "ymax": 102 / 1280},
-            "text": "table text",
-            "type": "Table",
-        }
+        [
+            {
+                "bbox": {"xmin": 1 / 1024, "ymin": 2 / 1280, "xmax": 101 / 1024, "ymax": 102 / 1280},
+                "text": "table text",
+                "type": "Table",
+            }
+        ]
     ]
 
     result = nemoretriever_parse(
         pdf_stream=sample_pdf_stream,
         extract_text=True,
         extract_images=False,
         extract_tables=True,
+        extract_charts=False,
         row_data=document_df.iloc[0],
         text_depth="page",
-        nemoretriever_parse_config=MagicMock(),
+        extract_tables_method="nemoretriever_parse",
+        nemoretriever_parse_config=mock_parser_config,
     )
 
     assert len(result) == 2
@@ -93,25 +108,29 @@ def test_nemoretriever_parse_table_extraction(mock_client, sample_pdf_stream, do
 
 
 @patch(f"{_MODULE_UNDER_TEST}.create_inference_client")
-def test_nemoretriever_parse_image_extraction(mock_client, sample_pdf_stream, document_df):
+def test_nemoretriever_parse_image_extraction(mock_client, sample_pdf_stream, document_df, mock_parser_config):
     mock_client_instance = MagicMock()
     mock_client.return_value = mock_client_instance
     mock_client_instance.infer.return_value = [
-        {
-            "bbox": {"xmin": 1 / 1024, "ymin": 2 / 1280, "xmax": 101 / 1024, "ymax": 102 / 1280},
-            "text": "",
-            "type": "Picture",
-        }
+        [
+            {
+                "bbox": {"xmin": 1 / 1024, "ymin": 2 / 1280, "xmax": 101 / 1024, "ymax": 102 / 1280},
+                "text": "",
+                "type": "Picture",
+            }
+        ]
     ]
 
     result = nemoretriever_parse(
         pdf_stream=sample_pdf_stream,
         extract_text=True,
         extract_images=True,
         extract_tables=False,
+        extract_charts=False,
         row_data=document_df.iloc[0],
         text_depth="page",
-        nemoretriever_parse_config=MagicMock(),
+        extract_tables_method="nemoretriever_parse",
+        nemoretriever_parse_config=mock_parser_config,
     )
 
     assert len(result) == 2
@@ -123,30 +142,34 @@ def test_nemoretriever_parse_image_extraction(mock_client, sample_pdf_stream, do
 
 
 @patch(f"{_MODULE_UNDER_TEST}.create_inference_client")
-def test_nemoretriever_parse_text_extraction_bboxes(mock_client, sample_pdf_stream, document_df):
+def test_nemoretriever_parse_text_extraction_bboxes(mock_client, sample_pdf_stream, document_df, mock_parser_config):
     mock_client_instance = MagicMock()
     mock_client.return_value = mock_client_instance
     mock_client_instance.infer.return_value = [
-        {
-            "bbox": {"xmin": 0.16633729456384325, "ymin": 0.0969, "xmax": 0.3097820480404551, "ymax": 0.1102},
-            "text": "testing0",
-            "type": "Title",
-        },
-        {
-            "bbox": {"xmin": 0.16633729456384325, "ymin": 0.0969, "xmax": 0.3097820480404551, "ymax": 0.1102},
-            "text": "testing1",
-            "type": "Text",
-        },
+        [
+            {
+                "bbox": {"xmin": 0.16633729456384325, "ymin": 0.0969, "xmax": 0.3097820480404551, "ymax": 0.1102},
+                "text": "testing0",
+                "type": "Title",
+            },
+            {
+                "bbox": {"xmin": 0.16633729456384325, "ymin": 0.0969, "xmax": 0.3097820480404551, "ymax": 0.1102},
+                "text": "testing1",
+                "type": "Text",
+            },
+        ]
     ]
 
     result = nemoretriever_parse(
         pdf_stream=sample_pdf_stream,
         extract_text=True,
         extract_images=False,
         extract_tables=False,
+        extract_charts=False,
         row_data=document_df.iloc[0],
         text_depth="page",
-        nemoretriever_parse_config=MagicMock(),
+        extract_tables_method="nemoretriever_parse",
+        nemoretriever_parse_config=mock_parser_config,
     )
 
     assert len(result) == 1

tests/nv_ingest/schemas/test_table_extractor_schema.py

@@ -7,49 +7,79 @@
 
 # Test cases for TableExtractorConfigSchema
 def test_valid_config_with_grpc_only():
-    config = TableExtractorConfigSchema(auth_token="valid_token", paddle_endpoints=("grpc://paddle_service", None))
+    config = TableExtractorConfigSchema(
+        auth_token="valid_token",
+        yolox_endpoints=("grpc://yolox_service", None),
+        paddle_endpoints=("grpc://paddle_service", None),
+    )
     assert config.auth_token == "valid_token"
+    assert config.yolox_endpoints == ("grpc://yolox_service", None)
     assert config.paddle_endpoints == ("grpc://paddle_service", None)
 
 
 def test_valid_config_with_http_only():
-    config = TableExtractorConfigSchema(auth_token="valid_token", paddle_endpoints=(None, "http://paddle_service"))
+    config = TableExtractorConfigSchema(
+        auth_token="valid_token",
+        yolox_endpoints=(None, "http://yolox_service"),
+        paddle_endpoints=(None, "http://paddle_service"),
+    )
     assert config.auth_token == "valid_token"
+    assert config.yolox_endpoints == (None, "http://yolox_service")
     assert config.paddle_endpoints == (None, "http://paddle_service")
 
 
 def test_valid_config_with_both_services():
     config = TableExtractorConfigSchema(
-        auth_token="valid_token", paddle_endpoints=("grpc://paddle_service", "http://paddle_service")
+        auth_token="valid_token",
+        yolox_endpoints=("grpc://yolox_service", "http://yolox_service"),
+        paddle_endpoints=("grpc://paddle_service", "http://paddle_service"),
     )
     assert config.auth_token == "valid_token"
+    assert config.yolox_endpoints == ("grpc://yolox_service", "http://yolox_service")
     assert config.paddle_endpoints == ("grpc://paddle_service", "http://paddle_service")
 
 
 def test_invalid_config_empty_endpoints():
     with pytest.raises(ValidationError) as exc_info:
-        TableExtractorConfigSchema(paddle_endpoints=(None, None))
+        TableExtractorConfigSchema(
+            yolox_endpoints=("grpc://yolox_service", "http://yolox_service"),
+            paddle_endpoints=(None, None),
+        )
     assert "Both gRPC and HTTP services cannot be empty for paddle_endpoints" in str(exc_info.value)
 
 
 def test_invalid_extra_fields():
     with pytest.raises(ValidationError) as exc_info:
         TableExtractorConfigSchema(
-            auth_token="valid_token", paddle_endpoints=("grpc://paddle_service", None), extra_field="invalid"
+            auth_token="valid_token",
+            yolox_endpoints=("grpc://yolox_service", None),
+            paddle_endpoints=("grpc://paddle_service", None),
+            extra_field="invalid",
         )
     assert "Extra inputs are not permitted" in str(exc_info.value)
 
 
 def test_cleaning_empty_strings_in_endpoints():
-    config = TableExtractorConfigSchema(paddle_endpoints=("   ", "http://paddle_service"))
+    config = TableExtractorConfigSchema(
+        yolox_endpoints=("grpc://yolox_service", " "),
+        paddle_endpoints=("   ", "http://paddle_service"),
+    )
+    assert config.yolox_endpoints == ("grpc://yolox_service", None)
     assert config.paddle_endpoints == (None, "http://paddle_service")
 
-    config = TableExtractorConfigSchema(paddle_endpoints=("grpc://paddle_service", ""))
+    config = TableExtractorConfigSchema(
+        yolox_endpoints=("", "http://yolox_service"),
+        paddle_endpoints=("grpc://paddle_service", ""),
+    )
+    assert config.yolox_endpoints == (None, "http://yolox_service")
     assert config.paddle_endpoints == ("grpc://paddle_service", None)
 
 
 def test_auth_token_is_none_by_default():
-    config = TableExtractorConfigSchema(paddle_endpoints=("grpc://paddle_service", "http://paddle_service"))
+    config = TableExtractorConfigSchema(
+        yolox_endpoints=("grpc://yolox_service", "http://yolox_service"),
+        paddle_endpoints=("grpc://paddle_service", "http://paddle_service"),
+    )
     assert config.auth_token is None
 
 
@@ -63,7 +93,10 @@ def test_table_extractor_schema_defaults():
 
 
 def test_table_extractor_schema_with_custom_values():
-    stage_config = TableExtractorConfigSchema(paddle_endpoints=("grpc://paddle_service", "http://paddle_service"))
+    stage_config = TableExtractorConfigSchema(
+        yolox_endpoints=("grpc://yolox_service", "http://yolox_service"),
+        paddle_endpoints=("grpc://paddle_service", "http://paddle_service"),
+    )
     config = TableExtractorSchema(max_queue_size=15, n_workers=12, raise_on_failure=True, stage_config=stage_config)
     assert config.max_queue_size == 15
     assert config.n_workers == 12

tests/nv_ingest/stages/nims/test_chart_extraction.py

@@ -120,7 +120,7 @@ def test_update_metadata_single_batch_single_worker(mocker, base64_image):
 
     # Patch join_yolox_and_paddle_output so that it returns a dict per image.
     mock_join = mocker.patch(
-        f"{MODULE_UNDER_TEST}.join_yolox_and_paddle_output",
+        f"{MODULE_UNDER_TEST}.join_yolox_graphic_elements_and_paddle_output",
         side_effect=[{"chart_title": "joined_1"}, {"chart_title": "joined_2"}],
     )
     # Patch process_yolox_graphic_elements to extract the chart title.
@@ -176,7 +176,7 @@ def test_update_metadata_multiple_batches_multi_worker(mocker, base64_image):
 
     # Patch join_yolox_and_paddle_output so it returns the expected joined dict per image.
     mock_join = mocker.patch(
-        f"{MODULE_UNDER_TEST}.join_yolox_and_paddle_output",
+        f"{MODULE_UNDER_TEST}.join_yolox_graphic_elements_and_paddle_output",
         side_effect=[{"chart_title": "joined_1"}, {"chart_title": "joined_2"}, {"chart_title": "joined_3"}],
     )
     # Patch process_yolox_graphic_elements to extract the chart title.