From 5ac19df046dff16bffc54b3ffb0214a16118ebd7 Mon Sep 17 00:00:00 2001
From: bwmac <bwm03570@gmail.com>
Date: Wed, 17 Jul 2024 11:19:31 -0600
Subject: [PATCH] clear notebook outputs

---
 gx_suite_definitions/network.ipynb | 937 +----------------------------
 1 file changed, 20 insertions(+), 917 deletions(-)

diff --git a/gx_suite_definitions/network.ipynb b/gx_suite_definitions/network.ipynb
index d2a769e6..ed04e37d 100644
--- a/gx_suite_definitions/network.ipynb
+++ b/gx_suite_definitions/network.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -32,42 +32,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Welcome, Brad Macdonald!\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "UPGRADE AVAILABLE\n",
-      "\n",
-      "A more recent version of the Synapse Client (4.3.0) is available. Your version (4.0.0) can be upgraded by typing:\n",
-      "    pip install --upgrade synapseclient\n",
-      "\n",
-      "Python Synapse Client version 4.3.0 release notes\n",
-      "\n",
-      "https://python-docs.synapse.org/news/\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "INFO: 2024-07-17 10:49:02 | synapseclient_default | Welcome, Brad Macdonald!\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "syn = synapseclient.Synapse()\n",
     "syn.login()\n"
@@ -75,7 +42,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -91,7 +58,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -102,69 +69,6 @@
     "validator.expectation_suite_name = \"network\""
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 28,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# get df rows where geneA_ensembl_gene_id is missing\n",
-    "df_missing = df[df['geneA_ensembl_gene_id'].isnull()]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 29,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1\" class=\"dataframe\">\n",
-       "  <thead>\n",
-       "    <tr style=\"text-align: right;\">\n",
-       "      <th></th>\n",
-       "      <th>geneA_ensembl_gene_id</th>\n",
-       "      <th>geneB_ensembl_gene_id</th>\n",
-       "      <th>geneA_external_gene_name</th>\n",
-       "      <th>geneB_external_gene_name</th>\n",
-       "      <th>brainRegion</th>\n",
-       "    </tr>\n",
-       "  </thead>\n",
-       "  <tbody>\n",
-       "  </tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "Empty DataFrame\n",
-       "Columns: [geneA_ensembl_gene_id, geneB_ensembl_gene_id, geneA_external_gene_name, geneB_external_gene_name, brainRegion]\n",
-       "Index: []"
-      ]
-     },
-     "execution_count": 29,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "df_missing.head()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -174,184 +78,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] <>:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | <>:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] <>:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | <>:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /var/folders/sr/3g4hnkfd4ld306tty7kqf1rr0000gr/T/ipykernel_84349/88841134.py:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "  validator.expect_column_values_to_match_regex(\"geneA_ensembl_gene_id\", \"^ENSG\\d{11}$\")\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | /var/folders/sr/3g4hnkfd4ld306tty7kqf1rr0000gr/T/ipykernel_84349/88841134.py:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "  validator.expect_column_values_to_match_regex(\"geneA_ensembl_gene_id\", \"^ENSG\\d{11}$\")\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "36d18115390a470288ba47b4e713e512",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/8 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "239af83a738f40998bd223c6275d394e",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/6 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "ea217354ad5e4192aa313be6c20436f5",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/8 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "{\n",
-       "  \"success\": true,\n",
-       "  \"result\": {\n",
-       "    \"element_count\": 347419,\n",
-       "    \"unexpected_count\": 0,\n",
-       "    \"unexpected_percent\": 0.0,\n",
-       "    \"partial_unexpected_list\": [],\n",
-       "    \"missing_count\": 0,\n",
-       "    \"missing_percent\": 0.0,\n",
-       "    \"unexpected_percent_total\": 0.0,\n",
-       "    \"unexpected_percent_nonmissing\": 0.0\n",
-       "  },\n",
-       "  \"meta\": {},\n",
-       "  \"exception_info\": {\n",
-       "    \"raised_exception\": false,\n",
-       "    \"exception_traceback\": null,\n",
-       "    \"exception_message\": null\n",
-       "  }\n",
-       "}"
-      ]
-     },
-     "execution_count": 19,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "# geneA_ensembl_gene_id\n",
     "validator.expect_column_values_to_be_of_type(\"geneA_ensembl_gene_id\", \"str\")\n",
@@ -361,184 +90,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] <>:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | <>:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] <>:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | <>:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /var/folders/sr/3g4hnkfd4ld306tty7kqf1rr0000gr/T/ipykernel_84349/4059227102.py:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "  validator.expect_column_values_to_match_regex(\"geneB_ensembl_gene_id\", \"^ENSG\\d{11}$\")\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | /var/folders/sr/3g4hnkfd4ld306tty7kqf1rr0000gr/T/ipykernel_84349/4059227102.py:4: DeprecationWarning: invalid escape sequence \\d\n",
-      "  validator.expect_column_values_to_match_regex(\"geneB_ensembl_gene_id\", \"^ENSG\\d{11}$\")\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:04 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "90af31de771f4ac0bb3ccf2f5dab23c0",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/8 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:05 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "93d80e188ced4dd8bdc9162dbfeb6786",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/6 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:05 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f925ccb6663540b4809fde09fa533027",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/8 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "{\n",
-       "  \"success\": true,\n",
-       "  \"result\": {\n",
-       "    \"element_count\": 347419,\n",
-       "    \"unexpected_count\": 0,\n",
-       "    \"unexpected_percent\": 0.0,\n",
-       "    \"partial_unexpected_list\": [],\n",
-       "    \"missing_count\": 0,\n",
-       "    \"missing_percent\": 0.0,\n",
-       "    \"unexpected_percent_total\": 0.0,\n",
-       "    \"unexpected_percent_nonmissing\": 0.0\n",
-       "  },\n",
-       "  \"meta\": {},\n",
-       "  \"exception_info\": {\n",
-       "    \"raised_exception\": false,\n",
-       "    \"exception_traceback\": null,\n",
-       "    \"exception_message\": null\n",
-       "  }\n",
-       "}"
-      ]
-     },
-     "execution_count": 20,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "# geneB_ensembl_gene_id\n",
     "validator.expect_column_values_to_be_of_type(\"geneB_ensembl_gene_id\", \"str\")\n",
@@ -548,134 +102,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:52:02 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "20b527163a5d41d1b2818858f64ae9af",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/8 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:52:02 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d4e27290eaae402fa5c8c2323323ffc0",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/6 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:52:02 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a5c471900ada493786d148a6711e48c7",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/9 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "{\n",
-       "  \"success\": true,\n",
-       "  \"result\": {\n",
-       "    \"element_count\": 347419,\n",
-       "    \"unexpected_count\": 0,\n",
-       "    \"unexpected_percent\": 0.0,\n",
-       "    \"partial_unexpected_list\": [],\n",
-       "    \"missing_count\": 318,\n",
-       "    \"missing_percent\": 0.09153212691303585,\n",
-       "    \"unexpected_percent_total\": 0.0,\n",
-       "    \"unexpected_percent_nonmissing\": 0.0\n",
-       "  },\n",
-       "  \"meta\": {},\n",
-       "  \"exception_info\": {\n",
-       "    \"raised_exception\": false,\n",
-       "    \"exception_traceback\": null,\n",
-       "    \"exception_message\": null\n",
-       "  }\n",
-       "}"
-      ]
-     },
-     "execution_count": 30,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "# geneA_external_gene_name\n",
     "validator.expect_column_values_to_be_of_type(\"geneA_external_gene_name\", \"str\")\n",
@@ -685,134 +114,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:06 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "053f03a2ec644e6298ae543982f3688b",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/8 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:06 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a9fb2cc4b16e4425a97237a266ae21c3",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/6 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:06 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "55cc3ebb6d024fa6884e1b823d67a071",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/9 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "{\n",
-       "  \"success\": true,\n",
-       "  \"result\": {\n",
-       "    \"element_count\": 347419,\n",
-       "    \"unexpected_count\": 0,\n",
-       "    \"unexpected_percent\": 0.0,\n",
-       "    \"partial_unexpected_list\": [],\n",
-       "    \"missing_count\": 216,\n",
-       "    \"missing_percent\": 0.06217276545036397,\n",
-       "    \"unexpected_percent_total\": 0.0,\n",
-       "    \"unexpected_percent_nonmissing\": 0.0\n",
-       "  },\n",
-       "  \"meta\": {},\n",
-       "  \"exception_info\": {\n",
-       "    \"raised_exception\": false,\n",
-       "    \"exception_traceback\": null,\n",
-       "    \"exception_message\": null\n",
-       "  }\n",
-       "}"
-      ]
-     },
-     "execution_count": 22,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "# geneB_external_gene_name\n",
     "validator.expect_column_values_to_be_of_type(\"geneB_external_gene_name\", \"str\")\n",
@@ -822,134 +126,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 23,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:07 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "90b5c89c0ad5439bbad4cd1b70a8d96c",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/8 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:07 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "090ec164fc4f4bcb81738156fd6fbae8",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/6 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:07 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a6ee61ac3e81487cad4122e78c35e521",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/8 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "{\n",
-       "  \"success\": true,\n",
-       "  \"result\": {\n",
-       "    \"element_count\": 347419,\n",
-       "    \"unexpected_count\": 0,\n",
-       "    \"unexpected_percent\": 0.0,\n",
-       "    \"partial_unexpected_list\": [],\n",
-       "    \"missing_count\": 0,\n",
-       "    \"missing_percent\": 0.0,\n",
-       "    \"unexpected_percent_total\": 0.0,\n",
-       "    \"unexpected_percent_nonmissing\": 0.0\n",
-       "  },\n",
-       "  \"meta\": {},\n",
-       "  \"exception_info\": {\n",
-       "    \"raised_exception\": false,\n",
-       "    \"exception_traceback\": null,\n",
-       "    \"exception_message\": null\n",
-       "  }\n",
-       "}"
-      ]
-     },
-     "execution_count": 23,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "# brainRegion\n",
     "validator.expect_column_values_to_be_of_type(\"brainRegion\", \"str\")\n",
@@ -959,70 +138,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 24,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "[WARNING] /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "WARNING: 2024-07-17 10:49:07 | py.warnings | /Users/bmacdonald/.local/share/virtualenvs/agora-data-tools-CK0oUlHB/lib/python3.9/site-packages/great_expectations/expectations/expectation.py:1481: UserWarning: `result_format` configured at the Validator-level will not be persisted. Please add the configuration to your Checkpoint config or checkpoint_run() method instead.\n",
-      "  warnings.warn(\n",
-      "\n"
-     ]
-    },
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "9d22a7910d2c4f43a2145d7784a6502a",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/7 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "data": {
-      "text/plain": [
-       "{\n",
-       "  \"success\": true,\n",
-       "  \"result\": {\n",
-       "    \"element_count\": 347419,\n",
-       "    \"unexpected_count\": 0,\n",
-       "    \"unexpected_percent\": 0.0,\n",
-       "    \"partial_unexpected_list\": [],\n",
-       "    \"missing_count\": 0,\n",
-       "    \"missing_percent\": 0.0,\n",
-       "    \"unexpected_percent_total\": 0.0,\n",
-       "    \"unexpected_percent_nonmissing\": 0.0\n",
-       "  },\n",
-       "  \"meta\": {},\n",
-       "  \"exception_info\": {\n",
-       "    \"raised_exception\": false,\n",
-       "    \"exception_traceback\": null,\n",
-       "    \"exception_message\": null\n",
-       "  }\n",
-       "}"
-      ]
-     },
-     "execution_count": 24,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "source": [
     "# multi-field\n",
     "validator.expect_compound_columns_to_be_unique([\"brainRegion\", \"geneA_ensembl_gene_id\", \"geneB_ensembl_gene_id\"])"
@@ -1037,7 +155,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1053,24 +171,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 26,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d5603e6306e14129b4ab4f85b52a7b3a",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Calculating Metrics:   0%|          | 0/86 [00:00<?, ?it/s]"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "checkpoint = context.add_or_update_checkpoint(\n",
     "    name=\"agora-test-checkpoint\",\n",