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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Vector Search "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import os, pandas as pd\n",
"from sqlalchemy import create_engine, text"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"username = 'demo'\n",
"password = 'demo'\n",
"hostname = os.getenv('IRIS_HOSTNAME', 'localhost')\n",
"port = '1972' \n",
"namespace = 'USER'\n",
"CONNECTION_STRING = f\"iris://{username}:{password}@{hostname}:{port}/{namespace}\"\n",
"\n",
"engine = create_engine(CONNECTION_STRING)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
"# Load knowledge graph\n",
"entity_embeddings = pd.read_csv('./entity_embeddings.csv', index_col=0)\n",
"entity_embeddings[\"embedding\"] = entity_embeddings[\"embedding\"].apply(\n",
" lambda x: x[1:-1])\n",
"\n",
"len_label = entity_embeddings['label'].str.len().max()\n",
"len_uri = entity_embeddings['uri'].str.len().max()\n",
"# TODO: set varchar length dynamically as above\n",
"with engine.connect() as conn:\n",
" with conn.begin(): \n",
" result = conn.execute(text('DROP TABLE IF EXISTS Test.EntityEmbeddings'))\n",
" sql = f\"\"\"\n",
" CREATE TABLE Test.EntityEmbeddings (\n",
" embedding VECTOR(DOUBLE, 50),\n",
" label VARCHAR({len_label}),\n",
" uri VARCHAR({len_uri})\n",
" )\n",
" \"\"\"\n",
" result = conn.execute(text(sql))\n",
"\n",
"with engine.connect() as conn:\n",
" with conn.begin():\n",
" for index, row in entity_embeddings.iterrows():\n",
" sql = text(\"\"\"\n",
" INSERT INTO Test.EntityEmbeddings \n",
" (embedding, label, uri) \n",
" VALUES (TO_VECTOR(:embedding), :label, :uri)\n",
" \"\"\")\n",
" conn.execute(sql, {\n",
" 'embedding': str(row['embedding']),\n",
" 'label': row['label'], \n",
" 'uri': row['uri']\n",
" })\n"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Exception during reset or similar\n",
"Traceback (most recent call last):\n",
" File \"/var/folders/g5/qwphv0rn5tvflncj75xsxvxw0000gn/T/ipykernel_77641/1077196279.py\", line 11, in <module>\n",
" result = conn.execute(text(sql))\n",
" ^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 1416, in execute\n",
" return meth(\n",
" ^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/sql/elements.py\", line 517, in _execute_on_connection\n",
" return connection._execute_clauseelement(\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 1639, in _execute_clauseelement\n",
" ret = self._execute_context(\n",
" ^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 1848, in _execute_context\n",
" return self._exec_single_context(\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 1988, in _exec_single_context\n",
" self._handle_dbapi_exception(\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 2347, in _handle_dbapi_exception\n",
" raise exc_info[1].with_traceback(exc_info[2])\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 1969, in _exec_single_context\n",
" self.dialect.do_execute(\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy_iris/base.py\", line 1060, in do_execute\n",
" cursor.execute(query, params)\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/dbapi/_DBAPI.py\", line 268, in execute\n",
" self._execute()\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/dbapi/_DBAPI.py\", line 528, in _execute\n",
" return exec_func()\n",
" ^^^^^^^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/dbapi/_DBAPI.py\", line 574, in _execute_query\n",
" self._send_direct_query_request()\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/dbapi/_DBAPI.py\", line 1159, in _send_direct_query_request\n",
" self._in_message._read_message_sql(sequence_number, self._statement_id, _InStream.FETCH_DATA, [100])\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py\", line 46, in _read_message_sql\n",
" is_for_gateway = self.__read_message_internal(expected_message_id, expected_statement_id, type)\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py\", line 59, in __read_message_internal\n",
" self.__read_buffer(header.buffer, 0, _MessageHeader.HEADER_SIZE)\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py\", line 146, in __read_buffer\n",
" raise Exception(\"Server unexpectedly closing communication device\")\n",
"Exception: Server unexpectedly closing communication device\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/var/folders/g5/qwphv0rn5tvflncj75xsxvxw0000gn/T/ipykernel_77641/1077196279.py\", line 3, in <module>\n",
" with conn.begin():\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/util.py\", line 161, in __exit__\n",
" self.rollback()\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 2599, in rollback\n",
" self._do_rollback()\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 2718, in _do_rollback\n",
" self._close_impl(try_deactivate=True)\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 2701, in _close_impl\n",
" self._connection_rollback_impl()\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 2693, in _connection_rollback_impl\n",
" self.connection._rollback_impl()\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 1121, in _rollback_impl\n",
" self._handle_dbapi_exception(e, None, None, None, None)\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 2347, in _handle_dbapi_exception\n",
" raise exc_info[1].with_traceback(exc_info[2])\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py\", line 1119, in _rollback_impl\n",
" self.engine.dialect.do_rollback(self.connection)\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy_iris/base.py\", line 1072, in do_rollback\n",
" connection.rollback()\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_IRISConnection.py\", line 494, in rollback\n",
" self._in_message._read_message_sql(sequence_number, -1, 0, [0])\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py\", line 46, in _read_message_sql\n",
" is_for_gateway = self.__read_message_internal(expected_message_id, expected_statement_id, type)\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py\", line 59, in __read_message_internal\n",
" self.__read_buffer(header.buffer, 0, _MessageHeader.HEADER_SIZE)\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py\", line 138, in __read_buffer\n",
" data = self._device.recv(length)\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_Device.py\", line 40, in recv\n",
" return self._socket.recv(len)\n",
" ^^^^^^^^^^^^^^^^^^^^^^\n",
"ConnectionResetError: [Errno 54] Connection reset by peer\n",
"\n",
"During handling of the above exception, another exception occurred:\n",
"\n",
"Traceback (most recent call last):\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/pool/base.py\", line 988, in _finalize_fairy\n",
" fairy._reset(\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/pool/base.py\", line 1438, in _reset\n",
" pool._dialect.do_rollback(self)\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy_iris/base.py\", line 1072, in do_rollback\n",
" connection.rollback()\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_IRISConnection.py\", line 493, in rollback\n",
" self._out_message._send(sequence_number)\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_OutStream.py\", line 18, in _send\n",
" self._device.sendall(self.wire._get_buffer())\n",
" File \"/Users/aldan.creo/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_Device.py\", line 37, in sendall\n",
" return self._socket.sendall(buffer)\n",
" ^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n",
"BrokenPipeError: [Errno 32] Broken pipe\n"
]
},
{
"ename": "ConnectionResetError",
"evalue": "[Errno 54] Connection reset by peer",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mException\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[19], line 11\u001b[0m\n\u001b[1;32m 4\u001b[0m sql \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[1;32m 5\u001b[0m \u001b[38;5;124m SELECT TOP 10 e1.uri AS uri1, e2.uri AS uri2, e1.label AS label1, e2.label AS label2,\u001b[39m\n\u001b[1;32m 6\u001b[0m \u001b[38;5;124m VECTOR_COSINE(e1.embedding, e2.embedding) AS distance\u001b[39m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[38;5;124m ORDER BY distance DESC\u001b[39m\n\u001b[1;32m 10\u001b[0m \u001b[38;5;124m \u001b[39m\u001b[38;5;124m\"\"\"\u001b[39m\n\u001b[0;32m---> 11\u001b[0m result \u001b[38;5;241m=\u001b[39m \u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtext\u001b[49m\u001b[43m(\u001b[49m\u001b[43msql\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 12\u001b[0m data \u001b[38;5;241m=\u001b[39m result\u001b[38;5;241m.\u001b[39mfetchall()\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:1416\u001b[0m, in \u001b[0;36mConnection.execute\u001b[0;34m(self, statement, parameters, execution_options)\u001b[0m\n\u001b[1;32m 1415\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1416\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mmeth\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1417\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1418\u001b[0m \u001b[43m \u001b[49m\u001b[43mdistilled_parameters\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1419\u001b[0m \u001b[43m \u001b[49m\u001b[43mexecution_options\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;129;43;01mor\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mNO_OPTIONS\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1420\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/sql/elements.py:517\u001b[0m, in \u001b[0;36mClauseElement._execute_on_connection\u001b[0;34m(self, connection, distilled_params, execution_options)\u001b[0m\n\u001b[1;32m 516\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(\u001b[38;5;28mself\u001b[39m, Executable)\n\u001b[0;32m--> 517\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mconnection\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_execute_clauseelement\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 518\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdistilled_params\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mexecution_options\u001b[49m\n\u001b[1;32m 519\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 520\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:1639\u001b[0m, in \u001b[0;36mConnection._execute_clauseelement\u001b[0;34m(self, elem, distilled_parameters, execution_options)\u001b[0m\n\u001b[1;32m 1631\u001b[0m compiled_sql, extracted_params, cache_hit \u001b[38;5;241m=\u001b[39m elem\u001b[38;5;241m.\u001b[39m_compile_w_cache(\n\u001b[1;32m 1632\u001b[0m dialect\u001b[38;5;241m=\u001b[39mdialect,\n\u001b[1;32m 1633\u001b[0m compiled_cache\u001b[38;5;241m=\u001b[39mcompiled_cache,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 1637\u001b[0m linting\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdialect\u001b[38;5;241m.\u001b[39mcompiler_linting \u001b[38;5;241m|\u001b[39m compiler\u001b[38;5;241m.\u001b[39mWARN_LINTING,\n\u001b[1;32m 1638\u001b[0m )\n\u001b[0;32m-> 1639\u001b[0m ret \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_execute_context\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1640\u001b[0m \u001b[43m \u001b[49m\u001b[43mdialect\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1641\u001b[0m \u001b[43m \u001b[49m\u001b[43mdialect\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecution_ctx_cls\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_init_compiled\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1642\u001b[0m \u001b[43m \u001b[49m\u001b[43mcompiled_sql\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1643\u001b[0m \u001b[43m \u001b[49m\u001b[43mdistilled_parameters\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1644\u001b[0m \u001b[43m \u001b[49m\u001b[43mexecution_options\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1645\u001b[0m \u001b[43m \u001b[49m\u001b[43mcompiled_sql\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1646\u001b[0m \u001b[43m \u001b[49m\u001b[43mdistilled_parameters\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1647\u001b[0m \u001b[43m \u001b[49m\u001b[43melem\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1648\u001b[0m \u001b[43m \u001b[49m\u001b[43mextracted_params\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1649\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_hit\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcache_hit\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1650\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1651\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m has_events:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:1848\u001b[0m, in \u001b[0;36mConnection._execute_context\u001b[0;34m(self, dialect, constructor, statement, parameters, execution_options, *args, **kw)\u001b[0m\n\u001b[1;32m 1847\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m-> 1848\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_exec_single_context\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1849\u001b[0m \u001b[43m \u001b[49m\u001b[43mdialect\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontext\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstatement\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparameters\u001b[49m\n\u001b[1;32m 1850\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:1988\u001b[0m, in \u001b[0;36mConnection._exec_single_context\u001b[0;34m(self, dialect, context, statement, parameters)\u001b[0m\n\u001b[1;32m 1987\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mBaseException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[0;32m-> 1988\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_handle_dbapi_exception\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1989\u001b[0m \u001b[43m \u001b[49m\u001b[43me\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstr_statement\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43meffective_parameters\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcursor\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontext\u001b[49m\n\u001b[1;32m 1990\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1992\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m result\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:2347\u001b[0m, in \u001b[0;36mConnection._handle_dbapi_exception\u001b[0;34m(self, e, statement, parameters, cursor, context, is_sub_exec)\u001b[0m\n\u001b[1;32m 2346\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m exc_info[\u001b[38;5;241m1\u001b[39m] \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m-> 2347\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m exc_info[\u001b[38;5;241m1\u001b[39m]\u001b[38;5;241m.\u001b[39mwith_traceback(exc_info[\u001b[38;5;241m2\u001b[39m])\n\u001b[1;32m 2348\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:1969\u001b[0m, in \u001b[0;36mConnection._exec_single_context\u001b[0;34m(self, dialect, context, statement, parameters)\u001b[0m\n\u001b[1;32m 1968\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m evt_handled:\n\u001b[0;32m-> 1969\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdialect\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdo_execute\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 1970\u001b[0m \u001b[43m \u001b[49m\u001b[43mcursor\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mstr_statement\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43meffective_parameters\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcontext\u001b[49m\n\u001b[1;32m 1971\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1973\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_has_events \u001b[38;5;129;01mor\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mengine\u001b[38;5;241m.\u001b[39m_has_events:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy_iris/base.py:1060\u001b[0m, in \u001b[0;36mIRISDialect.do_execute\u001b[0;34m(self, cursor, query, params, context)\u001b[0m\n\u001b[1;32m 1059\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_debug(query, params)\n\u001b[0;32m-> 1060\u001b[0m \u001b[43mcursor\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43mquery\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparams\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/dbapi/_DBAPI.py:268\u001b[0m, in \u001b[0;36m_BaseCursor.execute\u001b[0;34m(self, operation, params)\u001b[0m\n\u001b[1;32m 266\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cursor_type \u001b[38;5;241m=\u001b[39m CursorType\u001b[38;5;241m.\u001b[39mDEFAULT\n\u001b[0;32m--> 268\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_execute\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 269\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_rowcount\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/dbapi/_DBAPI.py:528\u001b[0m, in \u001b[0;36m_BaseCursor._execute\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 527\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 528\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mexec_func\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/dbapi/_DBAPI.py:574\u001b[0m, in \u001b[0;36m_BaseCursor._execute_query\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 572\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 573\u001b[0m \u001b[38;5;66;03m# not found in client side cache - send DQ message\u001b[39;00m\n\u001b[0;32m--> 574\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_send_direct_query_request\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 575\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/dbapi/_DBAPI.py:1159\u001b[0m, in \u001b[0;36mCursor._send_direct_query_request\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1158\u001b[0m \u001b[38;5;66;03m# retrieve data\u001b[39;00m\n\u001b[0;32m-> 1159\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_in_message\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_message_sql\u001b[49m\u001b[43m(\u001b[49m\u001b[43msequence_number\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_statement_id\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m_InStream\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mFETCH_DATA\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m100\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1160\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_sqlcode \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_in_message\u001b[38;5;241m.\u001b[39mwire\u001b[38;5;241m.\u001b[39mheader\u001b[38;5;241m.\u001b[39m_get_function_code()\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py:46\u001b[0m, in \u001b[0;36m_InStream._read_message_sql\u001b[0;34m(self, expected_message_id, expected_statement_id, type, allowedErrors)\u001b[0m\n\u001b[1;32m 45\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[0;32m---> 46\u001b[0m is_for_gateway \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__read_message_internal\u001b[49m\u001b[43m(\u001b[49m\u001b[43mexpected_message_id\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mexpected_statement_id\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mtype\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_for_gateway:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py:59\u001b[0m, in \u001b[0;36m_InStream.__read_message_internal\u001b[0;34m(self, expected_message_id, expected_statement_id, call_type)\u001b[0m\n\u001b[1;32m 58\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m high_bit \u001b[38;5;241m!=\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[0;32m---> 59\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__read_buffer\u001b[49m\u001b[43m(\u001b[49m\u001b[43mheader\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mbuffer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m_MessageHeader\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mHEADER_SIZE\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 60\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_log_stream \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py:146\u001b[0m, in \u001b[0;36m_InStream.__read_buffer\u001b[0;34m(self, buffer, offset, length)\u001b[0m\n\u001b[1;32m 145\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(data) \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[0;32m--> 146\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mServer unexpectedly closing communication device\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 147\u001b[0m buffer[offset\u001b[38;5;241m+\u001b[39mcb:offset\u001b[38;5;241m+\u001b[39mcb\u001b[38;5;241m+\u001b[39m\u001b[38;5;28mlen\u001b[39m(data)] \u001b[38;5;241m=\u001b[39m data\n",
"\u001b[0;31mException\u001b[0m: Server unexpectedly closing communication device",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mConnectionResetError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[19], line 3\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[38;5;66;03m# Calculate distance between entities\u001b[39;00m\n\u001b[1;32m 2\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m engine\u001b[38;5;241m.\u001b[39mconnect() \u001b[38;5;28;01mas\u001b[39;00m conn:\n\u001b[0;32m----> 3\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;28;43;01mwith\u001b[39;49;00m\u001b[43m \u001b[49m\u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mbegin\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\n\u001b[1;32m 4\u001b[0m \u001b[43m \u001b[49m\u001b[43msql\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;124;43mf\u001b[39;49m\u001b[38;5;124;43m\"\"\"\u001b[39;49m\n\u001b[1;32m 5\u001b[0m \u001b[38;5;124;43m SELECT TOP 10 e1.uri AS uri1, e2.uri AS uri2, e1.label AS label1, e2.label AS label2,\u001b[39;49m\n\u001b[1;32m 6\u001b[0m \u001b[38;5;124;43m VECTOR_COSINE(e1.embedding, e2.embedding) AS distance\u001b[39;49m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 9\u001b[0m \u001b[38;5;124;43m ORDER BY distance DESC\u001b[39;49m\n\u001b[1;32m 10\u001b[0m \u001b[38;5;124;43m \u001b[39;49m\u001b[38;5;124;43m\"\"\"\u001b[39;49m\n\u001b[1;32m 11\u001b[0m \u001b[43m \u001b[49m\u001b[43mresult\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtext\u001b[49m\u001b[43m(\u001b[49m\u001b[43msql\u001b[49m\u001b[43m)\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/util.py:161\u001b[0m, in \u001b[0;36mTransactionalContext.__exit__\u001b[0;34m(self, type_, value, traceback)\u001b[0m\n\u001b[1;32m 159\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 160\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_rollback_can_be_called():\n\u001b[0;32m--> 161\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrollback\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 162\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 163\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m out_of_band_exit:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:2599\u001b[0m, in \u001b[0;36mTransaction.rollback\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 2582\u001b[0m \u001b[38;5;250m\u001b[39m\u001b[38;5;124;03m\"\"\"Roll back this :class:`.Transaction`.\u001b[39;00m\n\u001b[1;32m 2583\u001b[0m \n\u001b[1;32m 2584\u001b[0m \u001b[38;5;124;03mThe implementation of this may vary based on the type of transaction in\u001b[39;00m\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 2596\u001b[0m \n\u001b[1;32m 2597\u001b[0m \u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 2598\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 2599\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_do_rollback\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2600\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 2601\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_active\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:2718\u001b[0m, in \u001b[0;36mRootTransaction._do_rollback\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 2717\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_do_rollback\u001b[39m(\u001b[38;5;28mself\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 2718\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_close_impl\u001b[49m\u001b[43m(\u001b[49m\u001b[43mtry_deactivate\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:2701\u001b[0m, in \u001b[0;36mRootTransaction._close_impl\u001b[0;34m(self, try_deactivate)\u001b[0m\n\u001b[1;32m 2699\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 2700\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mis_active:\n\u001b[0;32m-> 2701\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_connection_rollback_impl\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 2703\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconnection\u001b[38;5;241m.\u001b[39m_nested_transaction:\n\u001b[1;32m 2704\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconnection\u001b[38;5;241m.\u001b[39m_nested_transaction\u001b[38;5;241m.\u001b[39m_cancel()\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:2693\u001b[0m, in \u001b[0;36mRootTransaction._connection_rollback_impl\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 2692\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_connection_rollback_impl\u001b[39m(\u001b[38;5;28mself\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[0;32m-> 2693\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconnection\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_rollback_impl\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:1121\u001b[0m, in \u001b[0;36mConnection._rollback_impl\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1119\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mengine\u001b[38;5;241m.\u001b[39mdialect\u001b[38;5;241m.\u001b[39mdo_rollback(\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mconnection)\n\u001b[1;32m 1120\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mBaseException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[0;32m-> 1121\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_handle_dbapi_exception\u001b[49m\u001b[43m(\u001b[49m\u001b[43me\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:2347\u001b[0m, in \u001b[0;36mConnection._handle_dbapi_exception\u001b[0;34m(self, e, statement, parameters, cursor, context, is_sub_exec)\u001b[0m\n\u001b[1;32m 2345\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 2346\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m exc_info[\u001b[38;5;241m1\u001b[39m] \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[0;32m-> 2347\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m exc_info[\u001b[38;5;241m1\u001b[39m]\u001b[38;5;241m.\u001b[39mwith_traceback(exc_info[\u001b[38;5;241m2\u001b[39m])\n\u001b[1;32m 2348\u001b[0m \u001b[38;5;28;01mfinally\u001b[39;00m:\n\u001b[1;32m 2349\u001b[0m \u001b[38;5;28;01mdel\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reentrant_error\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy/engine/base.py:1119\u001b[0m, in \u001b[0;36mConnection._rollback_impl\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1117\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_log_info(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mROLLBACK\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 1118\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 1119\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mengine\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdialect\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mdo_rollback\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mconnection\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1120\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mBaseException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 1121\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_handle_dbapi_exception(e, \u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;28;01mNone\u001b[39;00m, \u001b[38;5;28;01mNone\u001b[39;00m)\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/sqlalchemy_iris/base.py:1072\u001b[0m, in \u001b[0;36mIRISDialect.do_rollback\u001b[0;34m(self, connection)\u001b[0m\n\u001b[1;32m 1071\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mdo_rollback\u001b[39m(\u001b[38;5;28mself\u001b[39m, connection):\n\u001b[0;32m-> 1072\u001b[0m \u001b[43mconnection\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrollback\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_IRISConnection.py:494\u001b[0m, in \u001b[0;36m_IRISConnection.rollback\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 492\u001b[0m sequence_number \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_get_new_sequence_number()\n\u001b[1;32m 493\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_out_message\u001b[38;5;241m.\u001b[39m_send(sequence_number)\n\u001b[0;32m--> 494\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_in_message\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_message_sql\u001b[49m\u001b[43m(\u001b[49m\u001b[43msequence_number\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m-\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py:46\u001b[0m, in \u001b[0;36m_InStream._read_message_sql\u001b[0;34m(self, expected_message_id, expected_statement_id, type, allowedErrors)\u001b[0m\n\u001b[1;32m 44\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_read_message_sql\u001b[39m(\u001b[38;5;28mself\u001b[39m, expected_message_id, expected_statement_id\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m-\u001b[39m\u001b[38;5;241m1\u001b[39m, \u001b[38;5;28mtype\u001b[39m\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m0\u001b[39m, allowedErrors\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m):\n\u001b[1;32m 45\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[0;32m---> 46\u001b[0m is_for_gateway \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__read_message_internal\u001b[49m\u001b[43m(\u001b[49m\u001b[43mexpected_message_id\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mexpected_statement_id\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mtype\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[1;32m 47\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_for_gateway:\n\u001b[1;32m 48\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_connection\u001b[38;5;241m.\u001b[39m_get_gateway()\u001b[38;5;241m.\u001b[39m_dispatch_reentrancy(\u001b[38;5;28mself\u001b[39m)\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py:59\u001b[0m, in \u001b[0;36m_InStream.__read_message_internal\u001b[0;34m(self, expected_message_id, expected_statement_id, call_type)\u001b[0m\n\u001b[1;32m 57\u001b[0m final_buffer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mbytearray\u001b[39m()\n\u001b[1;32m 58\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m high_bit \u001b[38;5;241m!=\u001b[39m \u001b[38;5;241m0\u001b[39m:\n\u001b[0;32m---> 59\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m__read_buffer\u001b[49m\u001b[43m(\u001b[49m\u001b[43mheader\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mbuffer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m_MessageHeader\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mHEADER_SIZE\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 60\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_log_stream \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 61\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_log_stream\u001b[38;5;241m.\u001b[39m_dump_header(\n\u001b[1;32m 62\u001b[0m header\u001b[38;5;241m.\u001b[39mbuffer, _LogFileStream\u001b[38;5;241m.\u001b[39mLOG_RECEIVED, \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_connection)\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_InStream.py:138\u001b[0m, in \u001b[0;36m_InStream.__read_buffer\u001b[0;34m(self, buffer, offset, length)\u001b[0m\n\u001b[1;32m 136\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_device \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 137\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mRuntimeError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mno longer connected to server\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m--> 138\u001b[0m data \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_device\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrecv\u001b[49m\u001b[43m(\u001b[49m\u001b[43mlength\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 139\u001b[0m buffer[offset:offset\u001b[38;5;241m+\u001b[39m\u001b[38;5;28mlen\u001b[39m(data)] \u001b[38;5;241m=\u001b[39m data\n\u001b[1;32m 140\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(data) \u001b[38;5;241m==\u001b[39m length:\n",
"File \u001b[0;32m~/miniconda3/envs/hackupc/lib/python3.11/site-packages/intersystems_iris/_Device.py:40\u001b[0m, in \u001b[0;36m_Device.recv\u001b[0;34m(self, len)\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mrecv\u001b[39m(\u001b[38;5;28mself\u001b[39m, \u001b[38;5;28mlen\u001b[39m):\n\u001b[0;32m---> 40\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_socket\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrecv\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mlen\u001b[39;49m\u001b[43m)\u001b[49m\n",
"\u001b[0;31mConnectionResetError\u001b[0m: [Errno 54] Connection reset by peer"
]
}
],
"source": [
"# Calculate distance between entities\n",
"with engine.connect() as conn:\n",
" with conn.begin():\n",
" sql = f\"\"\"\n",
" SELECT TOP 10 e1.uri AS uri1, e2.uri AS uri2, e1.label AS label1, e2.label AS label2,\n",
" VECTOR_COSINE(e1.embedding, e2.embedding) AS distance\n",
" FROM Test.EntityEmbeddings e1, Test.EntityEmbeddings e2\n",
" WHERE e1.uri = 'http://identifiers.org/medgen/C0002395'\n",
" ORDER BY distance DESC\n",
" \"\"\"\n",
" result = conn.execute(text(sql))\n",
" data = result.fetchall()\n",
" display(data)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Load clinical trials\n",
"\n",
"relation_embeddings = pd.read_csv('./relation_embeddings.csv', index_col=0)\n",
"relation_embeddings[\"embedding\"] = relation_embeddings[\"embedding\"].apply(\n",
" lambda x: x[1:-1])\n",
"\n",
"len_label = relation_embeddings['label'].str.len().max()\n",
"len_uri = relation_embeddings['uri'].str.len().max()\n",
"# TODO: set varchar length dynamically as above\n",
"with engine.connect() as conn:\n",
" with conn.begin():# Load \n",
" result = conn.execute(text('DROP TABLE IF EXISTS Test.RelationEmbeddings'))\n",
" sql = f\"\"\"\n",
" CREATE TABLE Test.RelationEmbeddings (\n",
" embedding VECTOR(DOUBLE, 50),\n",
" label VARCHAR({len_label}),\n",
" uri VARCHAR({len_uri})\n",
" )\n",
" \"\"\"\n",
" result = conn.execute(text(sql))\n",
"\n",
"with engine.connect() as conn:\n",
" with conn.begin():\n",
" for index, row in relation_embeddings.iterrows():\n",
" sql = text(\"\"\"\n",
" INSERT INTO Test.RelationEmbeddings \n",
" (embedding, label, uri) \n",
" VALUES (TO_VECTOR(:embedding), :label, :uri)\n",
" \"\"\")\n",
" conn.execute(sql, {\n",
" 'embedding': str(row['embedding']),\n",
" 'label': row['label'], \n",
" 'uri': row['uri']\n",
" })"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"# Load knowledge graph\n",
"clinical_trials = pd.read_csv(\"clinical_trials_embeddings.csv\")\n",
"clinical_trials[\"embeddings\"] = clinical_trials[\"embeddings\"].apply(lambda x: x[1:-1])\n",
"display(clinical_trials.head())\n",
"\n",
"# TODO: set varchar length dynamically as above\n",
"with engine.connect() as conn:\n",
" with conn.begin():\n",
" result = conn.execute(text(\"DROP TABLE IF EXISTS Test.ClinicalTrials\"))\n",
" sql = f\"\"\"\n",
" CREATE TABLE Test.ClinicalTrials (\n",
" nct_id VARCHAR(11) PRIMARY KEY,\n",
" diseases TEXT,\n",
" embedding VECTOR(DOUBLE, 768)\n",
" )\n",
" \"\"\"\n",
" result = conn.execute(text(sql))\n",
"\n",
"with engine.connect() as conn:\n",
" with conn.begin():\n",
" for index, row in clinical_trials.iterrows():\n",
"\n",
" sql = text(\n",
" \"\"\"\n",
" INSERT INTO Test.ClinicalTrials \n",
" (nct_id, diseases, embedding)\n",
" VALUES (:nct_id, :diseases, TO_VECTOR(:embedding))\n",
" \"\"\"\n",
" )\n",
" conn.execute(\n",
" sql,\n",
" {\n",
" \"nct_id\": row[\"nct_id\"],\n",
" \"diseases\": row[\"desease_condition\"],\n",
" \"embedding\": str(row[\"embeddings\"]),\n",
" },\n",
" )"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
" definition \\\n",
"0 A sudden onset of abdominal pain with associat... \n",
"1 A type of abdominal pain characterized by a fe... \n",
"2 Distention of the abdomen. \n",
"3 An abnormal enlargement or swelling in the abd... \n",
"4 New abnormal growth of tissue in the ABDOMEN. \n",
"\n",
" uri \\\n",
"0 http://identifiers.org/medgen/C0000727 \n",
"1 http://identifiers.org/medgen/C0000729 \n",
"2 http://identifiers.org/medgen/C0000731 \n",
"3 http://identifiers.org/medgen/C0000734 \n",
"4 http://identifiers.org/medgen/C0000735 \n",
"\n",
" embeddings \n",
"0 0.07821787893772125, 0.9349365234375, -0.11445... \n",
"1 -0.48267558217048645, 0.8518325090408325, -0.1... \n",
"2 -0.4706612527370453, -0.23200057446956635, -0.... \n",
"3 0.03700314462184906, 0.6256464123725891, -0.47... \n",
"4 -0.5286742448806763, 0.06493321806192398, -1.0... \n"
]
}
],
"source": [
"# %%\n",
"import pandas as pd\n",
"import rdflib\n",
"\n",
"# Load the disease descriptions from MGDEF.RRF\n",
"df_disease_descriptions = pd.read_csv(\"disease_descriptions_with_embeddings.csv\")\n",
"df_disease_descriptions[\"embeddings\"] = df_disease_descriptions[\"embeddings\"].apply(lambda x: x[1:-1])\n",
"\n",
"with engine.connect() as conn:\n",
" with conn.begin(): \n",
" result = conn.execute(text('DROP TABLE IF EXISTS Test.DiseaseDescriptions'))\n",
" sql = f\"\"\"\n",
" CREATE TABLE Test.DiseaseDescriptions (\n",
" definition TEXT,\n",
" uri TEXT,\n",
" embedding VECTOR(DOUBLE, 768)\n",
" )\n",
" \"\"\"\n",
" result = conn.execute(text(sql))\n",
"\n",
"with engine.connect() as conn:\n",
" with conn.begin():\n",
" for index, row in df_disease_descriptions.iterrows():\n",
" sql = text(\"\"\"\n",
" INSERT INTO Test.DiseaseDescriptions \n",
" (uri, definition, embedding)\n",
" VALUES (:uri, :definition, TO_VECTOR(:embedding))\n",
" \"\"\")\n",
" conn.execute(sql, {\n",
" 'uri': row['uri'],\n",
" 'definition': row['definition'],\n",
" 'embedding': str(row['embeddings'])\n",
" })"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "treehacks",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
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|