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[pull] master from CogStack:master #283

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Nov 26, 2024
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[pull] master from CogStack:master #283

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3d76a5d
CU-8696ent8k: vue3 upgrade and migration from bootstrap-vue UI framew…
tomolopolis Nov 3, 2024
7c49911
Merge pull request #220 from CogStack/vue3-upgrade
tomolopolis Nov 25, 2024
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269 changes: 196 additions & 73 deletions notebook_docs/API_Examples.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"import requests\n",
Expand All @@ -26,7 +28,9 @@
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"URL = 'http://localhost:8001' # Should be set to your running deployment, IP / PORT if not running on localhost:8001"
Expand All @@ -45,7 +49,9 @@
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"ortho_notes = pd.read_csv('example_data/ortho.csv')\n",
Expand All @@ -63,22 +69,24 @@
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"execution_count": 18,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/plain": [
"{'Authorization': 'Token cc3e60dd2cc4231f7f74d1f30d35ce31d3154f7c'}"
"{'Authorization': 'Token dece457ae382482d9edc999fdbf37dd39ea2893c'}"
]
},
"execution_count": 4,
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"payload = {\"username\": \"admin\", \"password\": \"admin\"}\n",
"payload = {\"username\": \"test\", \"password\": \"foobar312$\"}\n",
"headers = {\n",
" 'Authorization': f'Token {json.loads(requests.post(\"http://localhost:8001/api/api-token-auth/\", json=payload).text)[\"token\"]}',\n",
"}\n",
Expand All @@ -95,15 +103,18 @@
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"execution_count": 19,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/plain": [
"{'users': 'http://localhost:8001/api/users/',\n",
" 'entities': 'http://localhost:8001/api/entities/',\n",
" 'project-annotate-entities': 'http://localhost:8001/api/project-annotate-entities/',\n",
" 'project-groups': 'http://localhost:8001/api/project-groups/',\n",
" 'documents': 'http://localhost:8001/api/documents/',\n",
" 'annotated-entities': 'http://localhost:8001/api/annotated-entities/',\n",
" 'meta-annotations': 'http://localhost:8001/api/meta-annotations/',\n",
Expand All @@ -113,12 +124,10 @@
" 'entity-relations': 'http://localhost:8001/api/entity-relations/',\n",
" 'concept-dbs': 'http://localhost:8001/api/concept-dbs/',\n",
" 'vocabs': 'http://localhost:8001/api/vocabs/',\n",
" 'datasets': 'http://localhost:8001/api/datasets/',\n",
" 'icd-codes': 'http://localhost:8001/api/icd-codes/',\n",
" 'opcs-codes': 'http://localhost:8001/api/opcs-codes/'}"
" 'datasets': 'http://localhost:8001/api/datasets/'}"
]
},
"execution_count": 5,
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -143,63 +152,21 @@
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"metadata": {
"tags": []
},
"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>name</th>\n",
" <th>text</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>Subject 7</td>\n",
" <td>EXAM:,MRI LEFT KNEE WITHOUT CONTRAST,CLINICAL:...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>Subject 7</td>\n",
" <td>REASON FOR CONSULTATION: , Left hip fracture.,...</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>Subject 7</td>\n",
" <td>REASON FOR CONSULTATION: , Left hip fracture.,...</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" name text\n",
"0 Subject 7 EXAM:,MRI LEFT KNEE WITHOUT CONTRAST,CLINICAL:...\n",
"1 Subject 7 REASON FOR CONSULTATION: , Left hip fracture.,...\n",
"2 Subject 7 REASON FOR CONSULTATION: , Left hip fracture.,..."
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
"ename": "AttributeError",
"evalue": "'DataFrame' object has no attribute 'subject_id'",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m/tmp/ipykernel_10318/6590849.py\u001b[0m in \u001b[0;36m?\u001b[0;34m()\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;31m# Add a name column to the other datasets\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mortho_notes\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'name'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mortho_notes\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msubject_id\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0ml\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34mf'Subject {l}'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 3\u001b[0m \u001b[0mneuro_notes\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'name'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mneuro_notes\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msubject_id\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0ml\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34mf'Subject {l}'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 4\u001b[0;31m \u001b[0mcardio_notes\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'name'\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mcardio_notes\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msubject_id\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mapply\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;32mlambda\u001b[0m \u001b[0ml\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34mf'Subject {l}'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 5\u001b[0m \u001b[0mortho_notes\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mloc\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m'name'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'text'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mhead\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m3\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/miniconda3/envs/cattrainer/lib/python3.11/site-packages/pandas/core/generic.py\u001b[0m in \u001b[0;36m?\u001b[0;34m(self, name)\u001b[0m\n\u001b[1;32m 6200\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mname\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_accessors\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6201\u001b[0m \u001b[0;32mand\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_info_axis\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_can_hold_identifiers_and_holds_name\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 6202\u001b[0m ):\n\u001b[1;32m 6203\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mname\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 6204\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mobject\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m__getattribute__\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mname\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mAttributeError\u001b[0m: 'DataFrame' object has no attribute 'subject_id'"
]
}
],
"source": [
Expand All @@ -213,7 +180,9 @@
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# Collate datasets, with Names\n",
Expand Down Expand Up @@ -257,17 +226,171 @@
"#### Upload a CDB"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"tags": []
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"total 4020900\n",
"drwxrwxr-x 6 cerberus cerberus 4096 Jan 17 2024 20230227__kch_gstt_trained_model_494c3717f637bb89\n",
"-rw-rw-r-- 1 cerberus cerberus 954511008 Jan 17 2024 20230227__kch_gstt_trained_model_494c3717f637bb89.zip\n",
"-rw-r--r-- 1 cerberus cerberus 392429568 Jan 5 2024 cdb.dat\n",
"-rw-r--r-- 1 cerberus cerberus 607359360 Jun 7 2023 cdb-medmen.dat\n",
"drwxrwxr-x 4 cerberus cerberus 4096 Feb 8 2024 deid_medcat_n2c2_modelpack\n",
"-rw-r--r-- 1 cerberus cerberus 487520245 Feb 8 2024 deid_medcat_n2c2_modelpack.zip\n",
"-rw-r--r-- 1 cerberus cerberus 181988 Jan 5 2024 icd_11_cbd_utf8.dat\n",
"drwxrwxr-x 6 cerberus cerberus 4096 Feb 22 2024 medcat_model_pack_v1.4.0\n",
"-rw-rw-r-- 1 cerberus cerberus 841304525 Jan 5 2024 medcat_model_pack_v1.4.0.zip\n",
"-rw-r--r-- 1 cerberus cerberus 223 Jan 5 2024 pain_custom_cdb.dat\n",
"-rw-r--r-- 1 cerberus cerberus 25599 Jan 5 2024 pain_term.dat\n",
"-rw-r--r-- 1 cerberus cerberus 772635 Jan 5 2024 rxnorm_analgesic_cbd_utf8.dat\n",
"-rw-r--r-- 1 cerberus cerberus 362697 Jan 5 2024 rxnorm_analgesic_cbd_utf8_Y2VYjZO.dat\n",
"-rw-r--r-- 1 cerberus cerberus 832849835 Jan 5 2024 rxnorm_cdb.dat\n",
"-rw-rw-r-- 1 cerberus cerberus 21316 Aug 22 16:43 Untitled.ipynb\n"
]
}
],
"source": [
"!ls -l ../../medcat-models/cdb-medmen.dat"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"from medcat.cdb import CDB"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/plain": [
"<medcat.cdb.CDB at 0x704e66be4050>"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"CDB.load('../../medcat-models/deid_medcat_n2c2_modelpack/cdb.dat')"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"txt = json.loads(requests.post(f'{URL}/api/concept-dbs/', headers=headers, \n",
" data={'name': 'example_cdb', 'use_for_training': True}, \n",
" files={'cdb_file': open('../../medcat-models/deid_medcat_n2c2_modelpack/cdb.dat', 'rb')}).text)"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/plain": [
"{'id': 21,\n",
" 'name': 'example_cdb',\n",
" 'cdb_file': 'http://localhost:8001/media/cdb_HjbPPUI.dat',\n",
" 'use_for_training': True,\n",
" 'create_time': '2024-09-20T21:07:03.062580Z',\n",
" 'last_modified': '2024-09-20T21:07:03.062610Z',\n",
" 'last_modified_by': 1}"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"txt"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"txt = json.loads(requests.put(f'{URL}/api/concept-dbs/21/', headers=headers, \n",
" data={'name': 'example_cdb-EDITED', 'use_for_training': True}, \n",
" files={'cdb_file': open('../../medcat-models/deid_medcat_n2c2_modelpack/cdb.dat', 'rb')}).text)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {
"tags": []
},
"outputs": [
{
"data": {
"text/plain": [
"{'id': 21,\n",
" 'name': 'example_cdb',\n",
" 'cdb_file': 'http://localhost:8001/media/cdb_HjbPPUI.dat',\n",
" 'use_for_training': True,\n",
" 'create_time': '2024-09-20T21:07:03.062580Z',\n",
" 'last_modified': '2024-09-20T21:07:03.062610Z',\n",
" 'last_modified_by': 1}"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"txt = json.loads(requests.post(f'{URL}/api/concept-dbs/', headers=headers, \n",
"requests.post(f'{URL}/api/concept-dbs/', headers=headers, \n",
" data={'name': 'example_cdb', 'use_for_training': True}, \n",
" files={'cdb_file': open('<<LOCATION OF CDB>>', 'rb')}).text)"
" files={'cdb_file': open('../../medcat-models/deid_medcat_n2c2_modelpack/cdb.dat', 'rb')}).text)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -442,7 +565,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.8"
"version": "3.11.5"
}
},
"nbformat": 4,
Expand Down
11 changes: 3 additions & 8 deletions webapp/frontend/.editorconfig
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Original file line number Diff line number Diff line change
@@ -1,11 +1,6 @@
[*.{js,jsx,ts,tsx,vue}]
indent_style = space
[*.{js,jsx,mjs,cjs,ts,tsx,mts,cts,vue}]
charset = utf-8
indent_size = 2
trim_trailing_whitespace = true
insert_final_newline = true

[*.{js,jsx,ts,tsx,vue}]
indent_style = space
indent_size = 2
trim_trailing_whitespace = true
insert_final_newline = true
trim_trailing_whitespace = true
1 change: 0 additions & 1 deletion webapp/frontend/.env
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