FAQ

How do I release my own data with the ONE API?

First create a directory of ALF datasets, generate the cache tables, then share the directory with others. See data sharing guide for more information.

How do I use ONE without connecting to my database?

If you temporarily lose access to your Alyx database, you can instantiate ONE in local mode:

one = ONE(base_url='https://openalyx.internationalbrainlab.org', mode='local')

Why are my recent data missing from my cache but present on Alyx?

After new data are acquired it may take time for it to be copied to an online server (it will be marked as ‘online’ in Alyx). Once the data is marked as existing and online, it should appear in the cache tables next time they are generated. For the IBL Alyx, the ONE cache tables are re-generated every 6 hours, however by default ONE will only download a new cache once per day. To force a download you can run ONE().refresh_cache('remote'). More information, including increasing refresh frequency, can be found here.

Note: There are two different definitions of caches that are used in ONE2:

The cache table that stores info about all sessions and their associated datasets. This is refreshed every night and uploaded to Flatiron and downloaded onto your computer every 24hr (this is what the datetime object returned as output of the ONE().refresh_cache('remote') command is showing, i.e. when this cache was last updated). This table is used in all one.search, one.load, one.list functions. When doing ONE().refresh_cache('remote'), you are basically forcing ONE to re-download this table regardless of when it was last downloaded from Flatiron.
When running remote queries (anything that uses one.alyx.rest(....)), ONE stores the results of these queries for 24 hours, so that if you repeatedly make the same query over and over you don’t hit the database each time but can use the local cached result. A problem can arise if something on the Alyx database changes in between the same query:
- For example, at time X a given query returns an empty result (e.g. no histology session for a given subject). At time X+1, data is registered onto Alyx. At time X+2, you run the same query again. Because you had already made the query earlier, ONE uses the local result that it had previously and displays that there isn’t a histology session. To circumvent this, use the no_cache=True argument in one.alyx.rest(..., no_cache=True) or the no_cache web client context. More information can be found here. Use this only if necessary, as these methods are not optimized.

I made a mistake during setup and now can’t call setup, how do I fix it?

Usually you can re-run your setup with the following command:

from one.api import ONE
ONE.setup(base_url='https://alyx.example.com')

How do I change my download (a.k.a. cache) directory?

To permanently change the directory, simply re-run the setup routine:

from one.api import ONE
ONE.setup()  # Re-run setup for default database (takes effect next time you instantiate ONE)

When prompted (‘Enter the location of the download cache’) enter the absolute path of the new download location.

To temporarily change the download directory, use the cache_dir arg:

from pathlib import Path
from one.api import ONE

one = ONE(base_url='https://alyx.example.com', cache_dir=Path.home() / 'new_download_dir')

NB: This will (down)load the cache tables in the newly specified location. To avoid this, specify the cache table location separately using the tables_dir kwarg.

How do I load cache tables from a different location?

By default, the cache tables are in the cache_dir root. You can load cache tables in a different location in the following two ways:

from pathlib import Path
from one.api import ONE

# 1. Specify location upon instantiation
one = ONE(tables_dir=Path.home() / 'tables_dir')
# 2. Specify location after instantiation
one.load_cache(Path.home() / 'tables_dir')

NB: Avoid using the same location for different database cache tables: by default ONE will automatically overwrite tables when a newer version is available. To avoid automatic downloading, set mode='local'.

How do check who I’m logged in as?

from one.api import ONE
one = ONE()
if not one.offline:
    print(one.alyx.user)
    print(one.alyx.base_url)

How do I log out, or temporarily log in as someone else?

To log out:

from one.api import ONE
one = ONE()

one.alyx.logout()

To log in as someone else temporarily:

one.alyx.authenticate(username='other_user', cache_token=False, force=True)

What to do if I am seeing a certificate error?

If you are using the Windows platform, you may see a certificate error when initially trying to connect with ONE. The last few lines of the traceback should like this:

File "C:\Users\User\anaconda3\envs\ONE\lib\urllib\request.py", line 1351, in do_open
    raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:997)>

This has a relatively easy fix:

Open Microsoft Edge or Internet Explorer and navigate to the URL https://alyx.internationalbrainlab.org, or whichever alyx site you are attempting to access with ONE (no need to log in)
Reattempt to run any ONE query or setup on the command line
- Simply visiting the website with a Microsoft web browser should be enough to get the site’s certificate to be stored properly. This is a unique issue with the way that the Windows OS handles certificates.

How do I download the datasets cache for a specific IBL paper release?

You can download cache tables containing datasets with a specific release tag.

from one.api import ONE

one = ONE()
TAG = '2021_Q1_IBL_et_al_Behaviour'  # Release tag to download cache for
one.load_cache(tag=TAG)

To return to the full cache containing an index of all experiments:

ONE.cache_clear()
one = ONE()

How do I check which version of ONE I’m using within Python?

You can check your version with the following: print(ONE.version).
The latest version can be found in the CHANGELOG, here.
To update to the latest available version run pip install -U ONE-api.

How do I use ONE in a read-only environment?

To use ONE without any write access or internet access, simply instantiate in local mode:

from one.api import ONE
one = ONE(cache_dir='/path/to/data/dir', mode='local')
assert one.offline

If you wish to make Alyx database REST requests in a read-only environment, provide a database URL and set cache_rest=None to avoid saving REST responses on disk:

from one.api import ONE
one = ONE(base_url='https://openalyx.internationalbrainlab.org', cache_rest=None, mode='local')
assert one.offline and one.alyx.cache_mode is None

Why does the search return a LazyID object?

When in remote mode using one.search or one.search_insertions, a LazyID object is returned instead of a list. It behaves exactly the same as a list (you can index, slice and get its length). Instead of retrieving all the values from the database query it will fetch only the items you index from the list. This greatly speeds up the function when there are large search results.

How do I get information about a session from an experiment ID?

You can fetch a dictionary of experiment details from an experiment ID using the get_details method:

details = ONE().get_details(eid)

How do I search for sessions with the exact subject name (excluding partial matches)?

When not in remote mode you can use a regular expression to assert the start and end of the search string:

one = ONE(wildcards=True)  # Should be True by default
subject = 'FD_04'
eids = one.search(subject=f'^{subject}$')

When in remote mode you can use a Django exact query:

one = ONE(mode='remote')
subject = 'FD_04'
eids = one.search(django=f'subject__nickname__exact,{subject}')

Why are my search results inconsistent and/or seem to change?

This may be caused by one of two things:

First, each day when connecting to the database you download an updated cache table. The data on the database may simply have changed, or you are loading a different cache table from somewhere. This may be because you are connecting to a different database (check one.alyx.base_url), providing a different cache location (check one._tables_dir), or provided a different tag (see this question).

Second, there are minor differences between the default/local modes and remote mode. Namely that in remote mode queries are generally case-insensitive. See the ‘gotcha’ section of ‘Searching with ONE’ for more information.

How do I load datasets that pass quality control

You can first filter sessions by those that the supplied datasets with QC level WARNING or less:

one = ONE()
# In local and auto mode
eids = one.search(dataset=['trials', 'spikes'], dataset_qc_lte='WARNING')
# In remote mode
eids = one.search(datasets=['trials.table.pqt', 'spikes.times.npy'], dataset_qc_lte='WARNING')

You can then load the datasets with list_datasets and load_datasets:

dsets = one.list_datasets(eid, qc='WARNING', ignore_qc_not_set=True)
data, info = one.load_datasets(eid, dsets)