added bbox, fixed imports and bumped version

CONTRIBUTING.md

@@ -8,6 +8,7 @@ The key maintainers of this codebase are:
 - For small changes or a bug fixes, go ahead and create a PR
 - For large changes, create an issue on github with the proposal and @ one of the key maintainers for discussion before working on it
 - Run existing test cases and add test cases for changes to line_parser
+- Note that the ingestor tests are not yet runnable and have database dependencies (work in progress), so the likelihood of breaking things is very high
 
 ## Contribution areas
 - Make the new_indent_parser more accurate

nlm_ingestor/ingestion_daemon/__main__.py

@@ -64,7 +64,7 @@ def parse_document(
     return make_response(jsonify({"status": status, "reason": msg}), rc)
 
 def main():
-    logger.info("Starting parser service..")
+    logger.info("Starting ingestor service..")
     app.run(host="0.0.0.0", port=5001, debug=False)
 
 

nlm_ingestor/ingestor/visual_ingestor/block_renderer.py

@@ -255,6 +255,12 @@ def render_json(self):
                     "page_idx": block["page_idx"],
                     "block_class": block["block_class"],
                     "sentences": [block_text],
+                    "bbox": [
+                        block["box_style"][1],
+                        block["box_style"][0],
+                        block["box_style"][1] + block["box_style"][3],
+                        block["box_style"][0] + block["box_style"][4],
+                    ]                   
                 }
             elif block_type == "list_item" and not is_rendering_table:
                 block_dict = self.render_nested_block_as_dict(block, "list_item")
@@ -266,6 +272,12 @@ def render_json(self):
                     "page_idx": block["page_idx"],
                     "block_class": block["block_class"],
                     "sentences": [block_text],
+                    "bbox": [
+                        block["box_style"][1],
+                        block["box_style"][0],
+                        block["box_style"][1] + block["box_style"][3],
+                        block["box_style"][0] + block["box_style"][4],
+                    ]                   
                 }
 
             if block_dict:
@@ -329,7 +341,14 @@ def render_json(self):
 
             if 'is_table_end' in block:
                 is_rendering_table = False
-                render_dict["blocks"][-1]["table_rows"] = table_rows
+                table_block = render_dict["blocks"][-1] 
+                table_block["table_rows"] = table_rows
+                table_block["bbox"] = [
+                        table_block["left"],
+                        table_block["top"],
+                        table_block["left"] + block["box_style"][3],
+                        table_block["top"] + block["box_style"][4],
+                    ]                   
                 table_rows = []
 
         return render_dict
@@ -349,6 +368,12 @@ def render_nested_block_as_dict(self, block, tag):
                 "block_class": block["block_class"],
                 "sentences": [sent for sent in block["block_sents"]],
                 "block_idx": block["block_idx"],
+                "bbox": [
+                    block["box_style"][1],
+                    block["box_style"][0],
+                    block["box_style"][1] + block["box_style"][3],
+                    block["box_style"][0] + block["box_style"][4],
+                ]
             }
         return block_dict
 

nlm_ingestor/ingestor_utils/parsing_utils.py

@@ -131,7 +131,7 @@ def format_to_tr_block(prev_block, gap_threshold):
         child_x1 = child['box_style'][1]
 
         if gap_threshold <= round(child_x1 - prev_child_x2):
-            new_child_block = ingestor.visual_ingestor.Doc.merge_vls(block_buff)
+            new_child_block = nlm_ingestor.ingestor.visual_ingestor.Doc.merge_vls(block_buff)
             new_visual_lines.append(new_child_block)
             new_block_children.append({"text": block_text,
                                        "centroid": get_centroid(block_buff[0]['box_style'][1],
@@ -152,7 +152,7 @@ def format_to_tr_block(prev_block, gap_threshold):
                                                                 block_buff[-1]['box_style'][2]),
                                        "span": (prev_child['box_style'][1], child['box_style'][2])
                                        })
-            new_child_block = ingestor.visual_ingestor.Doc.merge_vls(block_buff)
+            new_child_block = nlm_ingestor.ingestor.visual_ingestor.Doc.merge_vls(block_buff)
             new_visual_lines.append(new_child_block)
     return new_block_children, new_visual_lines
 

notebooks/test_llmsherpa_api.ipynb

@@ -40,15 +40,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 27,
+   "execution_count": 61,
    "id": "d765b72f-5d58-4343-9f48-432acb31b7d6",
    "metadata": {},
    "outputs": [
     {
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/var/folders/10/036rtqts0zv6b9spnjgkl1hh0000gn/T/ipykernel_74969/2792954116.py:2: DeprecationWarning: Importing display from IPython.core.display is deprecated since IPython 7.14, please import from IPython display\n",
+      "/var/folders/10/036rtqts0zv6b9spnjgkl1hh0000gn/T/ipykernel_74969/3984827310.py:2: DeprecationWarning: Importing display from IPython.core.display is deprecated since IPython 7.14, please import from IPython display\n",
       "  from IPython.core.display import display, HTML\n"
      ]
     }
@@ -58,11 +58,11 @@
     "from IPython.core.display import display, HTML\n",
     "# llmsherpa_api_url = \"https://readers.llmsherpa.com/api/document/developer/parseDocument?renderFormat=all\"\n",
     "llmsherpa_api_url = \"http://localhost:5001/api/parseDocument?renderFormat=all\"\n",
-    "# pdf_url = \"https://arxiv.org/pdf/1910.13461.pdf\" # also allowed is a file path e.g. /home/downloads/xyz.pdf\n",
+    "pdf_url = \"https://arxiv.org/pdf/1910.13461.pdf\" # also allowed is a file path e.g. /home/downloads/xyz.pdf\n",
     "# pdf_url = \"https://www.apache.org/licenses/LICENSE-2.0.txt\"\n",
     "# pdf_url = \"https://microsoft.gcs-web.com/static-files/931d7780-ccfc-47e3-97ad-09d87e12b795\"\n",
     "# pdf_url = \"https://podcasts.ceu.edu/sites/podcasts.ceu.edu/files/sample.doc\"\n",
-    "pdf_url = \"/Users/ambikasukla/projects/data/Kubernetes.docx\"\n",
+    "# pdf_url = \"/Users/ambikasukla/projects/data/Kubernetes.docx\"\n",
     "# pdf_url = \"https://en.wikipedia.org/wiki/Language_model\"\n",
     "# pdf_url = \"https://raw.githubusercontent.com/nlmatics/llmsherpa/main/README.md\"\n",
     "# pdf_url = \"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=35362092&retmode=xml\"\n",
@@ -72,29 +72,30 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": 74,
    "id": "274fc39e-a574-4312-9d44-53b7758fa961",
    "metadata": {},
    "outputs": [
     {
      "data": {
-      "text/html": [
-       "<h1>NLMatics Kubernetes Cluster</h1><h2>1. Connect to the cluster.</h2><p>e.g.\n",
-       "to connect to LLMSherpa AKS.</p><p>2. List the pods</p><p>3. Log tailing for a specific pod</p><h2>4. Certificate Renewal</h2><p>· Delete the certificate.</p><p>· Delete the secret associated with the certificate.</p><p>· Restart the ingress-nginx-controller.</p><p>$ kubectl delete certificate tls-secret; kubectl delete secret tls-secret</p><p>Find the ingress-nginx-controller deployment file.</p><p>Edit the deployment file.</p><p>Modify the “replicas” to “0”.\n",
-       "Save and quit.</p><p>After 5 seconds, re-edit the file and modify the “replicas” back to 1.\n",
-       "Wait for ~30 seconds and the new certificate will be applied.</p>"
-      ],
       "text/plain": [
-       "<IPython.core.display.HTML object>"
+       "{'bbox': [179.52, 165.33, 421.01, 177.29000000000002],\n",
+       " 'block_class': 'cls_5',\n",
+       " 'block_idx': 2,\n",
+       " 'level': 1,\n",
+       " 'page_idx': 0,\n",
+       " 'sentences': ['{mikelewis,yinhanliu,naman}@fb.com'],\n",
+       " 'tag': 'header'}"
       ]
      },
-     "execution_count": 28,
+     "execution_count": 74,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "HTML(doc.sections()[0].to_html(include_children=True, recurse=True))"
+    "# HTML(doc.sections()[0].to_html(include_children=True, recurse=True))\n",
+    "doc.sections()[1].block_json"
    ]
   }
  ],

setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup, find_packages
 setup(
     name='nlm-ingestor',
-    version='0.1.1',    
+    version='0.1.2',    
     description='Parsers and ingestors for different file types and formats',
     long_description=open('README.md').read(),
     long_description_content_type='text/markdown',
@@ -11,7 +11,7 @@
     license='Apache License 2.0',
     packages=find_packages(),
     include_package_data=True,
-    package_data={'': ['ingestor_utils/*.txt']},
+    package_data={'': ['ingestor_utils/*.txt', ]},
     install_requires=[
         "flask",
         "flask_restful",

tests/run_ingestor_page_test.py

@@ -9,8 +9,8 @@
 from pymongo import MongoClient
 from tika import parser
 
-from ingestor import table_parser
-from ingestor import visual_ingestor
+from nlm_ingestor.ingestor import table_parser
+from nlm_ingestor.ingestor import visual_ingestor
 
 db_client = MongoClient(os.getenv("MONGO_HOST", "localhost"))
 db = db_client[os.getenv("MONGO_DATABASE", "doc-store-dev")]

tests/run_ingestor_table_tests.py

@@ -9,8 +9,8 @@
 from pymongo import MongoClient
 from tika import parser
 
-from ingestor import table_parser
-from ingestor import visual_ingestor
+from nlm_ingestor.ingestor import table_parser
+from nlm_ingestor.ingestor import visual_ingestor
 
 db_client = MongoClient(os.getenv("MONGO_HOST", "localhost"))
 db = db_client[os.getenv("MONGO_DATABASE", "doc-store-dev")]

tests/run_ingestor_test_full_doc.py

@@ -10,8 +10,8 @@
 from pymongo import MongoClient
 from tika import parser
 
-from ingestor import table_parser
-from ingestor import visual_ingestor
+from nlm_ingestor.ingestor import table_parser
+from nlm_ingestor.ingestor import visual_ingestor
 
 db_client = MongoClient(os.getenv("MONGO_HOST", "localhost"))
 db = db_client[os.getenv("MONGO_DATABASE", "doc-store-dev")]