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minrk/fetch-cgm-demo.ipynb

Created October 31, 2025 06:25
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fetch-cgm-demo.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 4,
"id": "bdd26a6d-5bab-4837-a5e9-7b8ec1853438",
"metadata": {},
"outputs": [],
"source": [
"patient_id = 40079\n",
"study_id = 30017"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "1e0046c6-9fc4-46a0-bf66-4dfb7413e8aa",
"metadata": {},
"outputs": [],
"source": [
"from jupyterhealth_client import JupyterHealthClient, Code\n",
"\n",
"jh_client = JupyterHealthClient()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "6538b63c-e7ee-4f4e-8c8e-82ad668f112c",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'id': 40079,\n",
" 'jheUserId': 10070,\n",
" 'identifier': '010101',\n",
" 'nameFamily': 'Doe',\n",
" 'nameGiven': 'Jane',\n",
" 'birthDate': '1998-01-01',\n",
" 'telecomPhone': None,\n",
" 'telecomEmail': '[email protected]',\n",
" 'organizations': [{'id': 20029,\n",
" 'name': 'JupyterCon Tutorial',\n",
" 'type': 'other',\n",
" 'partOf': 20028,\n",
" 'currentUserRole': None,\n",
" 'children': []}]}"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"jh_client.get_patient(patient_id)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "0ca50c78-c54a-48b7-9709-0bae745b74c9",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'id': 30017,\n",
" 'name': 'CGM sample data',\n",
" 'description': 'sample CGM data for JupyterCon tutorial',\n",
" 'organization': {'id': 20029, 'name': 'JupyterCon Tutorial', 'type': 'other'},\n",
" 'iconUrl': None}"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"jh_client.get_study(study_id)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "52c78b8b-5bad-4ff0-9611-d90dfc0465dd",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"4018\n"
]
},
{
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" <th></th>\n",
" <th>resource_type</th>\n",
" <th>code</th>\n",
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" <th>id</th>\n",
" <th>meta_lastUpdated</th>\n",
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" <th>blood_glucose_value</th>\n",
" <th>effective_time_frame_date_time</th>\n",
" <th>source_creation_date_time_local</th>\n",
" <th>effective_time_frame_date_time_local</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>Observation</td>\n",
" <td>158214</td>\n",
" <td>2025-10-31 04:43:00.293695+00:00</td>\n",
" <td>final</td>\n",
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" <td>https://www.freestyle.abbott/us-en/products/fr...</td>\n",
" <td>2025-10-29 20:16:53+00:00</td>\n",
" <td>mg/dL</td>\n",
" <td>102.0</td>\n",
" <td>2025-02-11 09:06:00+00:00</td>\n",
" <td>2025-10-29 20:16:53</td>\n",
" <td>2025-02-11 09:06:00</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>Observation</td>\n",
" <td>158213</td>\n",
" <td>2025-10-31 04:43:00.250402+00:00</td>\n",
" <td>final</td>\n",
" <td>Patient/40079</td>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>https://w3id.org/openmhealth</td>\n",
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" <td>https://www.freestyle.abbott/us-en/products/fr...</td>\n",
" <td>2025-10-29 20:16:53+00:00</td>\n",
" <td>mg/dL</td>\n",
" <td>107.0</td>\n",
" <td>2025-02-11 09:01:00+00:00</td>\n",
" <td>2025-10-29 20:16:53</td>\n",
" <td>2025-02-11 09:01:00</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>Observation</td>\n",
" <td>158212</td>\n",
" <td>2025-10-31 04:43:00.198434+00:00</td>\n",
" <td>final</td>\n",
" <td>Patient/40079</td>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>https://w3id.org/openmhealth</td>\n",
" <td>79571954-4b52-55a3-a2ef-d14dda039e82</td>\n",
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" <td>https://www.freestyle.abbott/us-en/products/fr...</td>\n",
" <td>2025-10-29 20:16:53+00:00</td>\n",
" <td>mg/dL</td>\n",
" <td>102.0</td>\n",
" <td>2025-02-11 08:56:00+00:00</td>\n",
" <td>2025-10-29 20:16:53</td>\n",
" <td>2025-02-11 08:56:00</td>\n",
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" <td>omh:blood-glucose:4.0</td>\n",
" <td>Observation</td>\n",
" <td>158211</td>\n",
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" <td>final</td>\n",
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" <td>omh:blood-glucose:4.0</td>\n",
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" <td>e7a41631-9dde-5dc2-832a-06375e8437bf</td>\n",
" <td>...</td>\n",
" <td>data source</td>\n",
" <td>https://www.libreview.com/</td>\n",
" <td>measuring device</td>\n",
" <td>https://www.freestyle.abbott/us-en/products/fr...</td>\n",
" <td>2025-10-29 20:16:53+00:00</td>\n",
" <td>mg/dL</td>\n",
" <td>97.0</td>\n",
" <td>2025-02-11 08:51:00+00:00</td>\n",
" <td>2025-10-29 20:16:53</td>\n",
" <td>2025-02-11 08:51:00</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>omh:blood-glucose:4.0</td>\n",
" <td>Observation</td>\n",
" <td>158210</td>\n",
" <td>2025-10-31 04:43:00.018684+00:00</td>\n",
" <td>final</td>\n",
" <td>Patient/40079</td>\n",
" <td>omh:blood-glucose:4.0</td>\n",
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" <td>https://www.freestyle.abbott/us-en/products/fr...</td>\n",
" <td>2025-10-29 20:16:53+00:00</td>\n",
" <td>mg/dL</td>\n",
" <td>93.0</td>\n",
" <td>2025-02-11 08:46:00+00:00</td>\n",
" <td>2025-10-29 20:16:53</td>\n",
" <td>2025-02-11 08:46:00</td>\n",
" </tr>\n",
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"</table>\n",
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"</div>"
],
"text/plain": [
" resource_type code resourceType id \\\n",
"0 omh:blood-glucose:4.0 omh:blood-glucose:4.0 Observation 158214 \n",
"1 omh:blood-glucose:4.0 omh:blood-glucose:4.0 Observation 158213 \n",
"2 omh:blood-glucose:4.0 omh:blood-glucose:4.0 Observation 158212 \n",
"3 omh:blood-glucose:4.0 omh:blood-glucose:4.0 Observation 158211 \n",
"4 omh:blood-glucose:4.0 omh:blood-glucose:4.0 Observation 158210 \n",
"\n",
" meta_lastUpdated status subject_reference \\\n",
"0 2025-10-31 04:43:00.293695+00:00 final Patient/40079 \n",
"1 2025-10-31 04:43:00.250402+00:00 final Patient/40079 \n",
"2 2025-10-31 04:43:00.198434+00:00 final Patient/40079 \n",
"3 2025-10-31 04:43:00.155407+00:00 final Patient/40079 \n",
"4 2025-10-31 04:43:00.018684+00:00 final Patient/40079 \n",
"\n",
" code_coding_0_code code_coding_0_system \\\n",
"0 omh:blood-glucose:4.0 https://w3id.org/openmhealth \n",
"1 omh:blood-glucose:4.0 https://w3id.org/openmhealth \n",
"2 omh:blood-glucose:4.0 https://w3id.org/openmhealth \n",
"3 omh:blood-glucose:4.0 https://w3id.org/openmhealth \n",
"4 omh:blood-glucose:4.0 https://w3id.org/openmhealth \n",
"\n",
" uuid ... \\\n",
"0 e0229319-528b-51b4-a696-b1d05209a0d9 ... \n",
"1 fedeb1e5-9789-5400-9981-6e05a8167117 ... \n",
"2 79571954-4b52-55a3-a2ef-d14dda039e82 ... \n",
"3 e7a41631-9dde-5dc2-832a-06375e8437bf ... \n",
"4 fb817f20-b18b-52e8-b82e-c93c463bfdea ... \n",
"\n",
" external_datasheets_0_datasheet_type \\\n",
"0 data source \n",
"1 data source \n",
"2 data source \n",
"3 data source \n",
"4 data source \n",
"\n",
" external_datasheets_0_datasheet_reference \\\n",
"0 https://www.libreview.com/ \n",
"1 https://www.libreview.com/ \n",
"2 https://www.libreview.com/ \n",
"3 https://www.libreview.com/ \n",
"4 https://www.libreview.com/ \n",
"\n",
" external_datasheets_1_datasheet_type \\\n",
"0 measuring device \n",
"1 measuring device \n",
"2 measuring device \n",
"3 measuring device \n",
"4 measuring device \n",
"\n",
" external_datasheets_1_datasheet_reference \\\n",
"0 https://www.freestyle.abbott/us-en/products/fr... \n",
"1 https://www.freestyle.abbott/us-en/products/fr... \n",
"2 https://www.freestyle.abbott/us-en/products/fr... \n",
"3 https://www.freestyle.abbott/us-en/products/fr... \n",
"4 https://www.freestyle.abbott/us-en/products/fr... \n",
"\n",
" source_creation_date_time blood_glucose_unit blood_glucose_value \\\n",
"0 2025-10-29 20:16:53+00:00 mg/dL 102.0 \n",
"1 2025-10-29 20:16:53+00:00 mg/dL 107.0 \n",
"2 2025-10-29 20:16:53+00:00 mg/dL 102.0 \n",
"3 2025-10-29 20:16:53+00:00 mg/dL 97.0 \n",
"4 2025-10-29 20:16:53+00:00 mg/dL 93.0 \n",
"\n",
" effective_time_frame_date_time source_creation_date_time_local \\\n",
"0 2025-02-11 09:06:00+00:00 2025-10-29 20:16:53 \n",
"1 2025-02-11 09:01:00+00:00 2025-10-29 20:16:53 \n",
"2 2025-02-11 08:56:00+00:00 2025-10-29 20:16:53 \n",
"3 2025-02-11 08:51:00+00:00 2025-10-29 20:16:53 \n",
"4 2025-02-11 08:46:00+00:00 2025-10-29 20:16:53 \n",
"\n",
" effective_time_frame_date_time_local \n",
"0 2025-02-11 09:06:00 \n",
"1 2025-02-11 09:01:00 \n",
"2 2025-02-11 08:56:00 \n",
"3 2025-02-11 08:51:00 \n",
"4 2025-02-11 08:46:00 \n",
"\n",
"[5 rows x 27 columns]"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"cgm = jh_client.list_observations_df(\n",
" patient_id=patient_id,\n",
" study_id=study_id,\n",
" code=Code.BLOOD_GLUCOSE.value,\n",
" limit=10_000,\n",
")\n",
"print(len(cgm))\n",
"cgm.head()"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "623eb956-f590-4149-8d09-1f1583a88b5f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"64\n"
]
},
{
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" <th>calories_unit</th>\n",
" <th>calories_value</th>\n",
" <th>food_name</th>\n",
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" <th>carbohydrate_unit</th>\n",
" <th>carbohydrate_value</th>\n",
" <th>effective_time_frame_date_time</th>\n",
" <th>source_creation_date_time_local</th>\n",
" <th>effective_time_frame_date_time_local</th>\n",
" <th>food_amount_unit</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>ieee:food-entry:0.1</td>\n",
" <td>ieee:food-entry:0.1</td>\n",
" <td>Observation</td>\n",
" <td>158278</td>\n",
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" <td>final</td>\n",
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" <td>...</td>\n",
" <td>kcal</td>\n",
" <td>317.71</td>\n",
" <td>Pumpkin Pie, single crust - 1/8 of 9\" pie</td>\n",
" <td>1.0</td>\n",
" <td>g</td>\n",
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" <td>...</td>\n",
" <td>kcal</td>\n",
" <td>147.67</td>\n",
" <td>Soy Milk, Vanilla or Other Flavors, Unsweetene...</td>\n",
" <td>2.0</td>\n",
" <td>g</td>\n",
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" <td>7396d38b-f46e-5081-b478-211e2d80c767</td>\n",
" <td>...</td>\n",
" <td>kcal</td>\n",
" <td>350.00</td>\n",
" <td>Sobey's, Nana's, Samosas, Chicken</td>\n",
" <td>1.0</td>\n",
" <td>g</td>\n",
" <td>35.0</td>\n",
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" <th>3</th>\n",
" <td>ieee:food-entry:0.1</td>\n",
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" <td>...</td>\n",
" <td>kcal</td>\n",
" <td>1.12</td>\n",
" <td>Lettuce, Iceberg, medium leaf</td>\n",
" <td>1.0</td>\n",
" <td>g</td>\n",
" <td>0.2</td>\n",
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" <td>ieee:food-entry:0.1</td>\n",
" <td>ieee:food-entry:0.1</td>\n",
" <td>Observation</td>\n",
" <td>158274</td>\n",
" <td>2025-10-31 04:43:32.287750+00:00</td>\n",
" <td>final</td>\n",
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" <td>...</td>\n",
" <td>kcal</td>\n",
" <td>317.71</td>\n",
" <td>Pumpkin Pie, single crust - 1/8 of 9\" pie</td>\n",
" <td>1.0</td>\n",
" <td>g</td>\n",
" <td>46.0</td>\n",
" <td>2025-02-10 10:10:00+00:00</td>\n",
" <td>2025-10-29 20:16:53</td>\n",
" <td>2025-02-10 10:10:00</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>5 rows × 27 columns</p>\n",
"</div>"
],
"text/plain": [
" resource_type code resourceType id \\\n",
"0 ieee:food-entry:0.1 ieee:food-entry:0.1 Observation 158278 \n",
"1 ieee:food-entry:0.1 ieee:food-entry:0.1 Observation 158277 \n",
"2 ieee:food-entry:0.1 ieee:food-entry:0.1 Observation 158276 \n",
"3 ieee:food-entry:0.1 ieee:food-entry:0.1 Observation 158275 \n",
"4 ieee:food-entry:0.1 ieee:food-entry:0.1 Observation 158274 \n",
"\n",
" meta_lastUpdated status subject_reference \\\n",
"0 2025-10-31 04:43:32.393599+00:00 final Patient/40079 \n",
"1 2025-10-31 04:43:32.368413+00:00 final Patient/40079 \n",
"2 2025-10-31 04:43:32.341884+00:00 final Patient/40079 \n",
"3 2025-10-31 04:43:32.314491+00:00 final Patient/40079 \n",
"4 2025-10-31 04:43:32.287750+00:00 final Patient/40079 \n",
"\n",
" code_coding_0_code code_coding_0_system \\\n",
"0 ieee:food-entry:0.1 https://w3id.org/openmhealth \n",
"1 ieee:food-entry:0.1 https://w3id.org/openmhealth \n",
"2 ieee:food-entry:0.1 https://w3id.org/openmhealth \n",
"3 ieee:food-entry:0.1 https://w3id.org/openmhealth \n",
"4 ieee:food-entry:0.1 https://w3id.org/openmhealth \n",
"\n",
" uuid ... calories_unit calories_value \\\n",
"0 5def8bb4-92e3-5cf0-9666-6a9c8deac30f ... kcal 317.71 \n",
"1 646fb4d4-8bea-5e66-ba08-56b67583e766 ... kcal 147.67 \n",
"2 7396d38b-f46e-5081-b478-211e2d80c767 ... kcal 350.00 \n",
"3 e1e27af0-2b18-5a00-b510-77a83f15b802 ... kcal 1.12 \n",
"4 f0a9087f-e55a-5377-ade9-04c269775212 ... kcal 317.71 \n",
"\n",
" food_name food_amount_value \\\n",
"0 Pumpkin Pie, single crust - 1/8 of 9\" pie 1.0 \n",
"1 Soy Milk, Vanilla or Other Flavors, Unsweetene... 2.0 \n",
"2 Sobey's, Nana's, Samosas, Chicken 1.0 \n",
"3 Lettuce, Iceberg, medium leaf 1.0 \n",
"4 Pumpkin Pie, single crust - 1/8 of 9\" pie 1.0 \n",
"\n",
" carbohydrate_unit carbohydrate_value effective_time_frame_date_time \\\n",
"0 g 46.0 2025-02-11 10:30:00+00:00 \n",
"1 g 6.0 2025-02-11 07:30:00+00:00 \n",
"2 g 35.0 2025-02-10 15:00:00+00:00 \n",
"3 g 0.2 2025-02-10 15:00:00+00:00 \n",
"4 g 46.0 2025-02-10 10:10:00+00:00 \n",
"\n",
" source_creation_date_time_local effective_time_frame_date_time_local \\\n",
"0 2025-10-29 20:16:53 2025-02-11 10:30:00 \n",
"1 2025-10-29 20:16:53 2025-02-11 07:30:00 \n",
"2 2025-10-29 20:16:53 2025-02-10 15:00:00 \n",
"3 2025-10-29 20:16:53 2025-02-10 15:00:00 \n",
"4 2025-10-29 20:16:53 2025-02-10 10:10:00 \n",
"\n",
" food_amount_unit \n",
"0 NaN \n",
"1 Cup \n",
"2 NaN \n",
"3 NaN \n",
"4 NaN \n",
"\n",
"[5 rows x 27 columns]"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"food = jh_client.list_observations_df(\n",
" patient_id=patient_id,\n",
" study_id=study_id,\n",
" code=Code.FOOD_ENTRY.value,\n",
")\n",
"print(len(food))\n",
"food.head()"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "61ffb15d-7b8d-4dc7-8a89-c64d06ed5c7c",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"14\n"
]
},
{
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" <td>Observation</td>\n",
" <td>158290</td>\n",
" <td>2025-10-31 04:43:34.109303+00:00</td>\n",
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],
"text/plain": [
" resource_type code resourceType \\\n",
"0 ieee:sleep-stage-summary:1.0 ieee:sleep-stage-summary:1.0 Observation \n",
"1 ieee:sleep-stage-summary:1.0 ieee:sleep-stage-summary:1.0 Observation \n",
"2 ieee:sleep-stage-summary:1.0 ieee:sleep-stage-summary:1.0 Observation \n",
"3 ieee:sleep-stage-summary:1.0 ieee:sleep-stage-summary:1.0 Observation \n",
"4 ieee:sleep-stage-summary:1.0 ieee:sleep-stage-summary:1.0 Observation \n",
"\n",
" id meta_lastUpdated status subject_reference \\\n",
"0 158292 2025-10-31 04:43:34.221920+00:00 final Patient/40079 \n",
"1 158291 2025-10-31 04:43:34.162794+00:00 final Patient/40079 \n",
"2 158290 2025-10-31 04:43:34.109303+00:00 final Patient/40079 \n",
"3 158289 2025-10-31 04:43:34.050193+00:00 final Patient/40079 \n",
"4 158288 2025-10-31 04:43:33.991443+00:00 final Patient/40079 \n",
"\n",
" code_coding_0_code code_coding_0_system \\\n",
"0 ieee:sleep-stage-summary:1.0 https://w3id.org/openmhealth \n",
"1 ieee:sleep-stage-summary:1.0 https://w3id.org/openmhealth \n",
"2 ieee:sleep-stage-summary:1.0 https://w3id.org/openmhealth \n",
"3 ieee:sleep-stage-summary:1.0 https://w3id.org/openmhealth \n",
"4 ieee:sleep-stage-summary:1.0 https://w3id.org/openmhealth \n",
"\n",
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"0 16fd8f95-8255-51ed-a323-32f1393a143d ... \n",
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"3 df15ccd3-a49c-5159-9c9b-9e32e7c485d9 ... \n",
"4 6706ebf5-2f34-541f-a184-f62dcc55b078 ... \n",
"\n",
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"3 NaT \n",
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"\n",
"[5 rows x 506 columns]"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sleep = jh_client.list_observations_df(\n",
" patient_id=patient_id,\n",
" study_id=study_id,\n",
" code=Code.SLEEP_STAGE_SUMMARY.value,\n",
")\n",
"print(len(sleep))\n",
"sleep.head()"
]
}
],
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