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Merge pull request #9 from individual-brain-charting/auth_fix
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Avoid repeated authentication when valid token is available
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@man-shu
man-shu committed Oct 6, 2023
2 parents d10099b + 29b65f0 commit 15897c5
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Showing 4 changed files with 106 additions and 69 deletions.
4 changes: 0 additions & 4 deletions README.md
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Expand Up @@ -23,10 +23,6 @@ db = ibc.get_info(data_type="volume_maps")
# Keep statistic maps for sub-08, for task-Discount
filtered_db = ibc.filter_data(db, subject_list=["08"], task_list=["Discount"])

# Authenticate with EBRAINS before downloading
# Returns a link that takes you to EBRAINS login page and stores an access token locally
ibc.authenticate()

# Download all statistic maps for sub-08, task-Discount
# Also creates ibc_data/downloaded_volume_maps.csv
# which contains local file paths and time of download
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4 changes: 0 additions & 4 deletions examples/example.py
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Expand Up @@ -7,10 +7,6 @@
# Keep statistic maps for sub-08, for task-Discount
filtered_db = ibc.filter_data(db, subject_list=["08"], task_list=["Discount"])

# Authenticate with EBRAINS before downloading
# Returns a link that takes you to EBRAINS login page and stores an access token locally
ibc.authenticate()

# Download all statistic maps for sub-08, task-Discount
# Also creates ibc_data/downloaded_volume_maps.csv
# which contains local file paths and time of download
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126 changes: 68 additions & 58 deletions examples/get_data.ipynb
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Expand Up @@ -28,7 +28,8 @@
"text": [
"[siibra:INFO] Version: 0.4a47\n",
"[siibra:WARNING] This is a development release. Use at your own risk.\n",
"[siibra:INFO] Please file bugs and issues at https://github.com/FZJ-INM1-BDA/siibra-python.\n"
"[siibra:INFO] Please file bugs and issues at https://github.com/FZJ-INM1-BDA/siibra-python.\n",
"[siibra:INFO] Clearing siibra cache at /home/himanshu/.cache/siibra.retrieval\n"
]
}
],
Expand Down Expand Up @@ -485,6 +486,13 @@
"execution_count": 5,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Found 12 files for subjects ['08'] and tasks ['Discount'].\n"
]
},
{
"data": {
"text/html": [
Expand Down Expand Up @@ -802,52 +810,54 @@
"cell_type": "markdown",
"metadata": {},
"source": [
"Now before we download these files, we need to authenticate with EBRAINS. This will return a link that takes you to EBRAINS login page and stores an access token locally.\n",
"\n"
"Now we are ready to download the few selected maps that we filtered.\n",
"\n",
"The following will save the requested maps under\n",
"``ibc_data/resulting_smooth_maps/sub-08/task-Discount`` \n",
"(or whatever subject you chose). And will also create a local CSV file ``ibc_data/downloaded_volume_maps.csv`` to track the downloaded files. This will contain local file paths and the time they were downloaded at, and is updated everytime you download new files.\n"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 9,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Found 12 files to download.\n",
"***\n",
"To continue, please go to https://iam.ebrains.eu/auth/realms/hbp/device?user_code=LGDW-XTRE\n",
"***\n",
"To continue, please go to https://iam.ebrains.eu/auth/realms/hbp/device?user_code=UFKZ-XXQU\n",
"***\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"[siibra:INFO] 139625 objects found for dataset ad04f919-7dcc-48d9-864a-d7b62af3d49d returned.\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"ebrains token successfuly set.\n"
]
}
],
"source": [
"ibc.authenticate()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we are ready to download the few selected maps that we filtered.\n",
"\n",
"The following will save the requested maps under\n",
"``ibc_data/resulting_smooth_maps/sub-08/task-Discount`` \n",
"(or whatever subject you chose). And will also create a local CSV file ``ibc_data/downloaded_volume_maps.csv`` to track the downloaded files. This will contain local file paths and the time they were downloaded at, and is updated everytime you download new files.\n"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"[siibra:INFO] 139625 objects found for dataset ad04f919-7dcc-48d9-864a-d7b62af3d49d returned.\n",
"12it [00:01, 11.22it/s]\n"
"\n",
"Overall Progress: 0%|\u001b[32m \u001b[0m| 0/12 [00:00<?, ?it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 17%|\u001b[32m██████████████████████████████████████████▌ \u001b[0m| 2/12 [00:00<00:00, 12.46it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 33%|\u001b[32m█████████████████████████████████████████████████████████████████████████████████████ \u001b[0m| 4/12 [00:00<00:00, 12.26it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 50%|\u001b[32m███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▌ \u001b[0m| 6/12 [00:00<00:00, 11.73it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 67%|\u001b[32m██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████ \u001b[0m| 8/12 [00:00<00:00, 11.80it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 83%|\u001b[32m███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████▋ \u001b[0m| 10/12 [00:00<00:00, 11.94it/s]\u001b[0m\u001b[A\n",
"Overall Progress: 100%|\u001b[32m██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████\u001b[0m| 12/12 [00:01<00:00, 11.97it/s]\u001b[0m\u001b[A\n"
]
},
{
Expand Down Expand Up @@ -886,62 +896,62 @@
" <tr>\n",
" <th>0</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.588770</td>\n",
" <td>2023-10-05 17:23:53.472528</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.765652</td>\n",
" <td>2023-10-05 17:23:53.628380</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.772669</td>\n",
" <td>2023-10-05 17:23:53.634523</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.944780</td>\n",
" <td>2023-10-05 17:23:53.793226</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:15.949580</td>\n",
" <td>2023-10-05 17:23:53.799418</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.116007</td>\n",
" <td>2023-10-05 17:23:53.972341</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.121902</td>\n",
" <td>2023-10-05 17:23:53.979429</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.298023</td>\n",
" <td>2023-10-05 17:23:54.140314</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.302662</td>\n",
" <td>2023-10-05 17:23:54.146809</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.471236</td>\n",
" <td>2023-10-05 17:23:54.304385</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.476903</td>\n",
" <td>2023-10-05 17:23:54.310566</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-...</td>\n",
" <td>2023-09-18 17:37:16.651207</td>\n",
" <td>2023-10-05 17:23:54.468429</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
Expand All @@ -963,21 +973,21 @@
"11 ibc_data/volume_maps/sub-08/ses-27/sub-08_ses-... \n",
"\n",
" downloaded_on \n",
"0 2023-09-18 17:37:15.588770 \n",
"1 2023-09-18 17:37:15.765652 \n",
"2 2023-09-18 17:37:15.772669 \n",
"3 2023-09-18 17:37:15.944780 \n",
"4 2023-09-18 17:37:15.949580 \n",
"5 2023-09-18 17:37:16.116007 \n",
"6 2023-09-18 17:37:16.121902 \n",
"7 2023-09-18 17:37:16.298023 \n",
"8 2023-09-18 17:37:16.302662 \n",
"9 2023-09-18 17:37:16.471236 \n",
"10 2023-09-18 17:37:16.476903 \n",
"11 2023-09-18 17:37:16.651207 "
"0 2023-10-05 17:23:53.472528 \n",
"1 2023-10-05 17:23:53.628380 \n",
"2 2023-10-05 17:23:53.634523 \n",
"3 2023-10-05 17:23:53.793226 \n",
"4 2023-10-05 17:23:53.799418 \n",
"5 2023-10-05 17:23:53.972341 \n",
"6 2023-10-05 17:23:53.979429 \n",
"7 2023-10-05 17:23:54.140314 \n",
"8 2023-10-05 17:23:54.146809 \n",
"9 2023-10-05 17:23:54.304385 \n",
"10 2023-10-05 17:23:54.310566 \n",
"11 2023-10-05 17:23:54.468429 "
]
},
"execution_count": 7,
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -996,16 +1006,16 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<nilearn.plotting.displays._slicers.OrthoSlicer at 0x7f341bf5fb80>"
"<nilearn.plotting.displays._slicers.OrthoSlicer at 0x7f7bdd436bb0>"
]
},
"execution_count": 8,
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
},
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41 changes: 38 additions & 3 deletions src/ibc_api/utils.py
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Expand Up @@ -3,6 +3,7 @@

import siibra
from siibra.retrieval.repositories import EbrainsHdgConnector
from siibra.retrieval.requests import EbrainsRequest, SiibraHttpRequestError
import os
from tqdm import tqdm
import nibabel
Expand All @@ -22,12 +23,37 @@
# all subjects in IBC dataset
SUBJECTS = md.SUBJECTS

# token root directory
TOKEN_ROOT = os.path.join(os.path.dirname(__file__), "data")
os.makedirs(TOKEN_ROOT, exist_ok=True)

def authenticate():

def _authenticate(token_dir=TOKEN_ROOT):
"""This function authenticates you to EBRAINS. It would return a link that
would prompt you to login or create an EBRAINS account. Read more about
registering for EBRAINS here: https://ebrains.eu/register"""
siibra.fetch_ebrains_token()
registering for EBRAINS here: https://ebrains.eu/register.
Once authenticated, it would store an access token locally in a token file and
use that token to connect to EBRAINS in the future. If the token expires, it
would prompt you to login again.
"""

# read the token file
token_file = os.path.join(token_dir, "token")
if os.path.exists(token_file):
with open(token_file, "r") as f:
token = f.read()
# set the token
siibra.set_ebrains_token(token)
else:
siibra.fetch_ebrains_token()
token = EbrainsRequest._KG_API_TOKEN
# save the token
with open(token_file, "w") as f:
f.write(token)

f.close()

return token_file


def _connect_ebrains(data_type="volume_maps", metadata=METADATA, version=None):
Expand Down Expand Up @@ -55,12 +81,21 @@ def _connect_ebrains(data_type="volume_maps", metadata=METADATA, version=None):
dataset = md.select_dataset(data_type, metadata, version)
dataset_id = dataset["id"]

# authenticate with ebrains
token_file = _authenticate()

try:
return EbrainsHdgConnector(dataset_id)
except AttributeError:
raise ValueError(
f"Unable to fetch dataset {data_type}, version {version} from EBRAINS."
)
except SiibraHttpRequestError:
print("Saved token is invalid. Fetching a new token.")
# delete the token file
os.remove(token_file)
# try connecting again
return _connect_ebrains(data_type, metadata, version)


def _create_root_dir(dir_path=None):
Expand Down

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