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nada-numpy Program for Whole-Genome Operations #72

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250 changes: 138 additions & 112 deletions services/nillion-interactor/large_dataset-test.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -101,8 +101,8 @@
"metadata": {
"collapsed": true,
"ExecuteTime": {
"end_time": "2024-08-22T13:57:21.425536Z",
"start_time": "2024-08-22T13:57:21.319781Z"
"end_time": "2024-09-13T19:17:01.391890Z",
"start_time": "2024-09-13T19:17:01.066083Z"
}
},
"source": [
Expand Down Expand Up @@ -163,8 +163,8 @@
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-08-22T14:24:49.198120Z",
"start_time": "2024-08-22T14:24:47.342660Z"
"end_time": "2024-09-13T19:17:07.083724Z",
"start_time": "2024-09-13T19:17:06.241704Z"
}
},
"cell_type": "code",
Expand All @@ -184,18 +184,18 @@
" [ 12184325, 1, 754105, 4]])"
]
},
"execution_count": 13,
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"execution_count": 13
"execution_count": 3
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-08-22T14:34:09.411111Z",
"start_time": "2024-08-22T14:34:09.406476Z"
"end_time": "2024-09-13T19:17:13.489386Z",
"start_time": "2024-09-13T19:17:13.483613Z"
}
},
"cell_type": "code",
Expand All @@ -208,12 +208,92 @@
"(631955, 4)"
]
},
"execution_count": 15,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"execution_count": 15
"execution_count": 4
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-09-13T19:17:16.699898Z",
"start_time": "2024-09-13T19:17:16.688849Z"
}
},
"cell_type": "code",
"source": "gene_data[gene_data[:, 0] == 1815739]",
"id": "a019086389c4aff",
"outputs": [
{
"data": {
"text/plain": [
"array([[ 1815739, 11, 66328095, 6]])"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"execution_count": 5
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-09-13T19:21:14.529977Z",
"start_time": "2024-09-13T19:21:14.464082Z"
}
},
"cell_type": "code",
"source": [
"target_snp_1 = 1815739\n",
"target_genotype_1 = 6\n",
"\n",
"boolean_mask = gene_data[:, 0] == target_snp_1\n",
"actual_genotype_1 = np.dot(boolean_mask, gene_data[:, 3])\n",
"actual_genotype_1"
],
"id": "4c536a0beca2655c",
"outputs": [
{
"data": {
"text/plain": [
"6"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"execution_count": 10
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-09-13T19:21:17.846807Z",
"start_time": "2024-09-13T19:21:17.842518Z"
}
},
"cell_type": "code",
"source": [
"\n",
"is_successful = actual_genotype_1 == target_genotype_1\n",
"print(is_successful)"
],
"id": "273585be787988f6",
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"True\n"
]
}
],
"execution_count": 11
},
{
"metadata": {},
Expand All @@ -229,6 +309,33 @@
}
},
"cell_type": "code",
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Loading environment variables from /Users/vishakh/.config/nillion/nillion-devnet.env\n",
"NILLION_CLUSTER_ID: 9e68173f-9c23-4acc-ba81-4f079b639964\n",
"NILLION_BOOTNODE_MULTIADDRESS: /ip4/127.0.0.1/tcp/37939/p2p/12D3KooWMvw1hEqm7EWSDEyqTb6pNetUVkepahKY6hixuAuMZfJS\n",
"NILLION_BOOTNODE_WEBSOCKET: /ip4/127.0.0.1/tcp/54936/ws/p2p/12D3KooWMvw1hEqm7EWSDEyqTb6pNetUVkepahKY6hixuAuMZfJS\n",
"NILLION_NILCHAIN_CHAIN_ID: nillion-chain-devnet\n",
"NILLION_NILCHAIN_JSON_RPC: http://127.0.0.1:48102\n",
"NILLION_NILCHAIN_REST_API: http://localhost:26650\n",
"NILLION_NILCHAIN_GRPC: localhost:26649\n",
"NILLION_NILCHAIN_PRIVATE_KEY_0: 9a975f567428d054f2bf3092812e6c42f901ce07d9711bc77ee2cd81101f42c5\n",
"NILLION_NILCHAIN_PRIVATE_KEY_1: 1e491133b9408b39572a29f91644873decea554224b20e2b0b923aeb860a1c18\n",
"NILLION_NILCHAIN_PRIVATE_KEY_2: 980488572f235316cdb330191f8bafe4e635efbe88b3a40f5bee9bd21047c059\n",
"NILLION_NILCHAIN_PRIVATE_KEY_3: 612bb5173dc60d9e91404fcc0d1f1847fb4459a7d5160d63d84e91aacbf2ab2f\n",
"NILLION_NILCHAIN_PRIVATE_KEY_4: 04f5a984eeea9dce4e5e907da69c01a61568e3071b1a91cbed89225f9fd913b5\n",
"NILLION_NILCHAIN_PRIVATE_KEY_5: 5f992c58921f4af83b4c6b650c4914626664cd02020577b0ada49cfa00d2c8a4\n",
"NILLION_NILCHAIN_PRIVATE_KEY_6: 8f0297d3bb647eb59b95b29550b2aebbedd9be2c954b000e772efe8c9318a42d\n",
"NILLION_NILCHAIN_PRIVATE_KEY_7: c395243df9bb68dc809668efe4125f0eb017771ed8e3747b8d6860551913fecb\n",
"NILLION_NILCHAIN_PRIVATE_KEY_8: 4bb5eaa799e24ae2b48545c41331921afe7e6a8dd7a850f5fbeb20a8226664ec\n",
"NILLION_NILCHAIN_PRIVATE_KEY_9: ef4b944d4fdb0077057925fe2dde365dfa2c83cf320463b14589feccd1b2b938\n"
]
}
],
"execution_count": 47,
"source": [
"import os\n",
"import py_nillion_client as nillion\n",
Expand Down Expand Up @@ -267,34 +374,7 @@
" prefix=\"nillion\",\n",
")"
],
"id": "84da614cf4520b6c",
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Loading environment variables from /Users/vishakh/.config/nillion/nillion-devnet.env\n",
"NILLION_CLUSTER_ID: 9e68173f-9c23-4acc-ba81-4f079b639964\n",
"NILLION_BOOTNODE_MULTIADDRESS: /ip4/127.0.0.1/tcp/37939/p2p/12D3KooWMvw1hEqm7EWSDEyqTb6pNetUVkepahKY6hixuAuMZfJS\n",
"NILLION_BOOTNODE_WEBSOCKET: /ip4/127.0.0.1/tcp/54936/ws/p2p/12D3KooWMvw1hEqm7EWSDEyqTb6pNetUVkepahKY6hixuAuMZfJS\n",
"NILLION_NILCHAIN_CHAIN_ID: nillion-chain-devnet\n",
"NILLION_NILCHAIN_JSON_RPC: http://127.0.0.1:48102\n",
"NILLION_NILCHAIN_REST_API: http://localhost:26650\n",
"NILLION_NILCHAIN_GRPC: localhost:26649\n",
"NILLION_NILCHAIN_PRIVATE_KEY_0: 9a975f567428d054f2bf3092812e6c42f901ce07d9711bc77ee2cd81101f42c5\n",
"NILLION_NILCHAIN_PRIVATE_KEY_1: 1e491133b9408b39572a29f91644873decea554224b20e2b0b923aeb860a1c18\n",
"NILLION_NILCHAIN_PRIVATE_KEY_2: 980488572f235316cdb330191f8bafe4e635efbe88b3a40f5bee9bd21047c059\n",
"NILLION_NILCHAIN_PRIVATE_KEY_3: 612bb5173dc60d9e91404fcc0d1f1847fb4459a7d5160d63d84e91aacbf2ab2f\n",
"NILLION_NILCHAIN_PRIVATE_KEY_4: 04f5a984eeea9dce4e5e907da69c01a61568e3071b1a91cbed89225f9fd913b5\n",
"NILLION_NILCHAIN_PRIVATE_KEY_5: 5f992c58921f4af83b4c6b650c4914626664cd02020577b0ada49cfa00d2c8a4\n",
"NILLION_NILCHAIN_PRIVATE_KEY_6: 8f0297d3bb647eb59b95b29550b2aebbedd9be2c954b000e772efe8c9318a42d\n",
"NILLION_NILCHAIN_PRIVATE_KEY_7: c395243df9bb68dc809668efe4125f0eb017771ed8e3747b8d6860551913fecb\n",
"NILLION_NILCHAIN_PRIVATE_KEY_8: 4bb5eaa799e24ae2b48545c41331921afe7e6a8dd7a850f5fbeb20a8226664ec\n",
"NILLION_NILCHAIN_PRIVATE_KEY_9: ef4b944d4fdb0077057925fe2dde365dfa2c83cf320463b14589feccd1b2b938\n"
]
}
],
"execution_count": 47
"id": "84da614cf4520b6c"
},
{
"metadata": {},
Expand All @@ -310,6 +390,8 @@
}
},
"cell_type": "code",
"outputs": [],
"execution_count": 48,
"source": [
"from typing import Any\n",
"import nada_numpy.client as na_client\n",
Expand Down Expand Up @@ -346,9 +428,7 @@
" )\n",
" return store_id"
],
"id": "2740bbe472dbdffb",
"outputs": [],
"execution_count": 48
"id": "2740bbe472dbdffb"
},
{
"metadata": {},
Expand All @@ -364,22 +444,6 @@
}
},
"cell_type": "code",
"source": [
"permissions = nillion.Permissions.default_for_user(monadic_user_id)\n",
"\n",
"store_id = await store_secret_array(\n",
" monadic_client,\n",
" payments_wallet,\n",
" payments_client,\n",
" cluster_id,\n",
" gene_data,\n",
" \"gene_data\",\n",
" nillion.SecretInteger,\n",
" 1,\n",
" permissions,\n",
")"
],
"id": "ad961c332478c206",
"outputs": [
{
"name": "stdout",
Expand All @@ -402,7 +466,23 @@
]
}
],
"execution_count": 49
"execution_count": 49,
"source": [
"permissions = nillion.Permissions.default_for_user(monadic_user_id)\n",
"\n",
"store_id = await store_secret_array(\n",
" monadic_client,\n",
" payments_wallet,\n",
" payments_client,\n",
" cluster_id,\n",
" gene_data,\n",
" \"gene_data\",\n",
" nillion.SecretInteger,\n",
" 1,\n",
" permissions,\n",
")"
],
"id": "ad961c332478c206"
},
{
"metadata": {},
Expand All @@ -419,60 +499,6 @@
],
"id": "755c0d8d6ef4ceb6"
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-08-22T14:41:58.625914Z",
"start_time": "2024-08-22T14:41:58.616792Z"
}
},
"cell_type": "code",
"source": "gene_data[gene_data[:, 0] == 1815739]",
"id": "a019086389c4aff",
"outputs": [
{
"data": {
"text/plain": [
"array([[ 1815739, 11, 66328095, 6]])"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"execution_count": 16
},
{
"metadata": {
"ExecuteTime": {
"end_time": "2024-08-22T14:44:11.011121Z",
"start_time": "2024-08-22T14:44:11.003410Z"
}
},
"cell_type": "code",
"source": [
"target_snp_1 = 1815739\n",
"target_genotype_1 = 9\n",
"\n",
"rows_of_interest = gene_data[gene_data[:, 0] == target_snp_1]\n",
"is_successful = rows_of_interest[0, 3] == target_genotype_1\n",
"print(rows_of_interest)\n",
"print(is_successful)"
],
"id": "273585be787988f6",
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"[[ 1815739 11 66328095 6]]\n",
"False\n"
]
}
],
"execution_count": 21
},
{
"metadata": {},
"cell_type": "markdown",
Expand Down
9 changes: 4 additions & 5 deletions services/nillion-interactor/programs/muscle-perform-array.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,8 @@ def nada_main():
party1 = Party(name="Party1")

gene_data = na.array((1, 4), party1, "gene_data", SecretInteger)
rows_of_interest = gene_data[gene_data[:, 0] == target_snp_1]
is_successful = rows_of_interest[0, 3] == target_genotype_1
boolean_mask = gene_data[:, 0] == target_snp_1
actual_genotype_1 = boolean_mask.dot(gene_data[:, 3])
is_successful = actual_genotype_1 == target_genotype_1

result = is_successful.reveal()

return [Output(result, "Result", party1)]
return [Output(is_successful, "Result", party1)]
1 change: 1 addition & 0 deletions services/nillion-interactor/requirements.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
python-dotenv==1.0.0
nada-dsl==0.6.0
nada-numpy==0.5.2
py-nillion-client==0.6.0
pytest-asyncio>=0.23.6
Flask[async]==3.0.3
Expand Down