Query & search registries¶
Find & access data using registries.
Setup¶
!lamin init --storage ./mydata
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💡 connected lamindb: testuser1/mydata
import lamindb as ln
ln.settings.verbosity = "info"
💡 connected lamindb: testuser1/mydata
We’ll need some toy data:
ln.Artifact(ln.core.datasets.file_jpg_paradisi05(), description="My image").save()
ln.Artifact.from_df(ln.core.datasets.df_iris(), description="The iris collection").save()
ln.Artifact(ln.core.datasets.file_fastq(), description="My fastq").save()
Show code cell output
❗ no run & transform get linked, consider calling ln.track()
✅ storing artifact 'r6QrYNk2tYOJNCeE8OGU' at '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/r6QrYNk2tYOJNCeE8OGU.jpg'
❗ no run & transform get linked, consider calling ln.track()
✅ storing artifact 'kYLiZUoFQoyEHYUNZScq' at '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/kYLiZUoFQoyEHYUNZScq.parquet'
❗ no run & transform get linked, consider calling ln.track()
✅ storing artifact 'lhO04hY93JAfnFQXgKwV' at '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/lhO04hY93JAfnFQXgKwV.fastq.gz'
Artifact(uid='lhO04hY93JAfnFQXgKwV', description='My fastq', suffix='.fastq.gz', type='dataset', size=20, hash='hi7ZmAzz8sfMd3vIQr-57Q', hash_type='md5', visibility=1, key_is_virtual=True, created_by_id=1, storage_id=1, updated_at='2024-06-19 16:17:13 UTC')
Look up metadata¶
For entities where we don’t store more than 100k records, a look up object can be a convenient way of selecting a record.
Consider the User registry:
users = ln.User.lookup(field="handle")
With auto-complete, we find a user:
user = users.testuser1
user
User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at='2024-06-19 16:17:11 UTC')
Note
You can also auto-complete in a dictionary:
users_dict = ln.User.lookup().dict()
Filter by metadata¶
Filter for all artifacts created by a user:
ln.Artifact.filter(created_by=user).df()
| uid | version | description | key | suffix | type | accessor | size | hash | hash_type | n_objects | n_observations | visibility | key_is_virtual | storage_id | transform_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 1 | r6QrYNk2tYOJNCeE8OGU | None | My image | None | .jpg | dataset | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.125355+00:00 |
| 2 | kYLiZUoFQoyEHYUNZScq | None | The iris collection | None | .parquet | dataset | DataFrame | 5629 | ah24lV9Ncc8nPL0MumEsdw | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.265187+00:00 |
| 3 | lhO04hY93JAfnFQXgKwV | None | My fastq | None | .fastq.gz | dataset | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.272914+00:00 |
To access the results encoded in a filter statement, execute its return value with one of:
.df(): A pandasDataFramewith each record stored as a row..all(): An indexable djangoQuerySet..list(): A list of records..one(): Exactly one record. Will raise an error if there is none..one_or_none(): Either one record orNoneif there is no query result.
Note
The ORMs in LaminDB are Django Models and any Django query works. LaminDB extends Django’s API for data scientists.
Under the hood, any .filter() call translates into a SQL select statement.
.one() and .one_or_none() are two parts of LaminDB’s API that are borrowed from SQLAlchemy.
Search for metadata¶
ln.Artifact.search("iris").df()
| uid | version | description | key | suffix | type | accessor | size | hash | hash_type | n_objects | n_observations | visibility | key_is_virtual | storage_id | transform_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 2 | kYLiZUoFQoyEHYUNZScq | None | The iris collection | None | .parquet | dataset | DataFrame | 5629 | ah24lV9Ncc8nPL0MumEsdw | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.265187+00:00 |
Let us create 500 notebook objects with fake titles and save them:
ln.save(
[
ln.Transform(name=title, type="notebook")
for title in ln.core.datasets.fake_bio_notebook_titles(n=500)
]
)
We can now search for any combination of terms:
ln.Transform.search("intestine").df().head()
| uid | version | name | key | description | type | reference | reference_type | latest_report_id | source_code_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | 549CThD1JsS9ucxN | None | Igg2 intestinal intestine cluster. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.417329+00:00 |
| 9 | GUIgBqSZVIzVbI0i | None | Intestine IgG4 IgA study IgG3 result. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.418670+00:00 |
| 13 | X1oFmAFdiellRw57 | None | Intestine Brunner's gland IgG3 candidate IgA S... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.419302+00:00 |
| 22 | r8uOjrJEiNSWqLvy | None | Igg4 Ovaries Vulva intestine visualize IgD Cho... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.420753+00:00 |
| 42 | TBepG1gJSqKcHtxQ | None | Iga IgG4 result Bowman's gland intestine IgG4 ... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.423941+00:00 |
Leverage relations¶
Django has a double-under-score syntax to filter based on related tables.
This syntax enables you to traverse several layers of relations:
ln.Artifact.filter(run__created_by__handle__startswith="testuse").df()
| uid | version | description | key | suffix | type | accessor | size | hash | hash_type | n_objects | n_observations | visibility | key_is_virtual | storage_id | transform_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id |
The filter selects all artifacts based on the users who ran the generating notebook.
(Under the hood, in the SQL database, it’s joining the artifact table with the run and the user table.)
Beyond __startswith, Django supports about two dozen field comparators field__comparator=value.
Here are some of them.
and¶
ln.Artifact.filter(suffix=".jpg", created_by=user).df()
| uid | version | description | key | suffix | type | accessor | size | hash | hash_type | n_objects | n_observations | visibility | key_is_virtual | storage_id | transform_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 1 | r6QrYNk2tYOJNCeE8OGU | None | My image | None | .jpg | dataset | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.125355+00:00 |
less than/ greater than¶
Or subset to artifacts greater than 10kB. Here, we can’t use keyword arguments, but need an explicit where statement.
ln.Artifact.filter(created_by=user, size__lt=1e4).df()
| uid | version | description | key | suffix | type | accessor | size | hash | hash_type | n_objects | n_observations | visibility | key_is_virtual | storage_id | transform_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 2 | kYLiZUoFQoyEHYUNZScq | None | The iris collection | None | .parquet | dataset | DataFrame | 5629 | ah24lV9Ncc8nPL0MumEsdw | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.265187+00:00 |
| 3 | lhO04hY93JAfnFQXgKwV | None | My fastq | None | .fastq.gz | dataset | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.272914+00:00 |
or¶
from django.db.models import Q
ln.Artifact.filter().filter(Q(suffix=".jpg") | Q(suffix=".fastq.gz")).df()
| uid | version | description | key | suffix | type | accessor | size | hash | hash_type | n_objects | n_observations | visibility | key_is_virtual | storage_id | transform_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 1 | r6QrYNk2tYOJNCeE8OGU | None | My image | None | .jpg | dataset | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.125355+00:00 |
| 3 | lhO04hY93JAfnFQXgKwV | None | My fastq | None | .fastq.gz | dataset | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.272914+00:00 |
in¶
ln.Artifact.filter(suffix__in=[".jpg", ".fastq.gz"]).df()
| uid | version | description | key | suffix | type | accessor | size | hash | hash_type | n_objects | n_observations | visibility | key_is_virtual | storage_id | transform_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 1 | r6QrYNk2tYOJNCeE8OGU | None | My image | None | .jpg | dataset | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.125355+00:00 |
| 3 | lhO04hY93JAfnFQXgKwV | None | My fastq | None | .fastq.gz | dataset | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.272914+00:00 |
order by¶
ln.Artifact.filter().order_by("-updated_at").df()
| uid | version | description | key | suffix | type | accessor | size | hash | hash_type | n_objects | n_observations | visibility | key_is_virtual | storage_id | transform_id | run_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 3 | lhO04hY93JAfnFQXgKwV | None | My fastq | None | .fastq.gz | dataset | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.272914+00:00 |
| 2 | kYLiZUoFQoyEHYUNZScq | None | The iris collection | None | .parquet | dataset | DataFrame | 5629 | ah24lV9Ncc8nPL0MumEsdw | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.265187+00:00 |
| 1 | r6QrYNk2tYOJNCeE8OGU | None | My image | None | .jpg | dataset | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-19 16:17:13.125355+00:00 |
contains¶
ln.Transform.filter(name__contains="search").df().head(10)
| uid | version | name | key | description | type | reference | reference_type | latest_report_id | source_code_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 8 | DgPauDDek6ing5ET | None | Ige IgG IgG3 IgG1 Joints research Choroid plexus. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.418513+00:00 |
| 10 | kmU7BpSb8D6hU09H | None | Research visualize research classify. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.418828+00:00 |
| 12 | 8PeyNQl6OssoaKtz | None | Bowman'S Gland research IgD result investigate... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.419144+00:00 |
| 27 | 6dDm2YSAI9iRPkcG | None | Hyalocyte Basal cell (stem cell) IgG1 research... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.421551+00:00 |
| 30 | WZygMSTXG8wnOTmS | None | Igg4 IgG4 research Ovaries cluster IgD IgG2. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.422047+00:00 |
| 31 | fpS6OO10CUafEfta | None | Joints Outer root sheath IgG4 IgG4 research. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.422205+00:00 |
| 35 | Fai70OPERcURJ1NU | None | Research IgD IgG3 IgG4 efficiency efficiency. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.422838+00:00 |
| 44 | YcQPJ3OfBcekuYxW | None | Olfactory Ensheathing Cells efficiency IgG3 re... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.424256+00:00 |
| 52 | Lwt3m7ftFsKvFsRo | None | Investigate investigate IgA Planum semilunatum... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.425513+00:00 |
| 68 | pFaHp3msWeEqt4iO | None | Research study Joints visualize IgG IgG2. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.428042+00:00 |
And case-insensitive:
ln.Transform.filter(name__icontains="Search").df().head(10)
| uid | version | name | key | description | type | reference | reference_type | latest_report_id | source_code_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 8 | DgPauDDek6ing5ET | None | Ige IgG IgG3 IgG1 Joints research Choroid plexus. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.418513+00:00 |
| 10 | kmU7BpSb8D6hU09H | None | Research visualize research classify. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.418828+00:00 |
| 12 | 8PeyNQl6OssoaKtz | None | Bowman'S Gland research IgD result investigate... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.419144+00:00 |
| 27 | 6dDm2YSAI9iRPkcG | None | Hyalocyte Basal cell (stem cell) IgG1 research... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.421551+00:00 |
| 30 | WZygMSTXG8wnOTmS | None | Igg4 IgG4 research Ovaries cluster IgD IgG2. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.422047+00:00 |
| 31 | fpS6OO10CUafEfta | None | Joints Outer root sheath IgG4 IgG4 research. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.422205+00:00 |
| 35 | Fai70OPERcURJ1NU | None | Research IgD IgG3 IgG4 efficiency efficiency. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.422838+00:00 |
| 44 | YcQPJ3OfBcekuYxW | None | Olfactory Ensheathing Cells efficiency IgG3 re... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.424256+00:00 |
| 52 | Lwt3m7ftFsKvFsRo | None | Investigate investigate IgA Planum semilunatum... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.425513+00:00 |
| 68 | pFaHp3msWeEqt4iO | None | Research study Joints visualize IgG IgG2. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.428042+00:00 |
startswith¶
ln.Transform.filter(name__startswith="Research").df()
| uid | version | name | key | description | type | reference | reference_type | latest_report_id | source_code_id | created_by_id | updated_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 10 | kmU7BpSb8D6hU09H | None | Research visualize research classify. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.418828+00:00 |
| 35 | Fai70OPERcURJ1NU | None | Research IgD IgG3 IgG4 efficiency efficiency. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.422838+00:00 |
| 68 | pFaHp3msWeEqt4iO | None | Research study Joints visualize IgG IgG2. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.428042+00:00 |
| 125 | veUslvVshfEwCZxN | None | Research Joints IgA visualize. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.439955+00:00 |
| 184 | qY8yEpzUfHsenHfF | None | Research Brunner's gland Joints IgA. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.451583+00:00 |
| 229 | nqet7PB0VbrowWLe | None | Research IgA Heat-sensitive sensory neurons Br... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.460955+00:00 |
| 277 | RExU4WoIdO7gbMCS | None | Research IgE Ovaries IgG4. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.468234+00:00 |
| 278 | XkGP6liA4US87xC3 | None | Research efficiency IgG3 IgG3. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.468383+00:00 |
| 281 | dTEwcclYMZlwCol9 | None | Research intestinal candidate IgD IgG4 intesti... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.468828+00:00 |
| 315 | A9Rvyc360aOAGY2s | None | Research Schwann cells intestinal investigate ... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.476506+00:00 |
| 379 | gjP3hspK2mEGOd4A | None | Research Hyalocyte research intestinal IgA. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.486090+00:00 |
| 388 | QYomthPtw2WZF201 | None | Research Planum semilunatum epithelial cell of... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.490041+00:00 |
| 472 | oXY8Hk8yBOTW55WG | None | Research Bowman's gland IgG3 cluster IgG4. | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.505119+00:00 |
| 499 | dKmu5NDLiDyq10Dy | None | Research Bowman's gland IgG4 Basal cell (stem ... | None | None | notebook | None | None | None | None | 1 | 2024-06-19 16:17:18.509206+00:00 |
Show code cell content
# clean up test instance
!lamin delete --force mydata
!rm -r mydata
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.11.9/x64/bin/lamin", line 8, in <module>
sys.exit(main())
^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/rich_click/rich_command.py", line 367, in __call__
return super().__call__(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/rich_click/rich_command.py", line 152, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/lamin_cli/__main__.py", line 103, in delete
return delete(instance, force=force)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/lamindb_setup/_delete.py", line 98, in delete
n_objects = check_storage_is_empty(
^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/lamindb_setup/core/upath.py", line 779, in check_storage_is_empty
raise InstanceNotEmpty(message)
lamindb_setup.core.upath.InstanceNotEmpty: Storage /home/runner/work/lamindb/lamindb/docs/mydata/.lamindb contains 3 objects ('_is_initialized' ignored) - delete them prior to deleting the instance
['/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/_is_initialized', '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/kYLiZUoFQoyEHYUNZScq.parquet', '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/lhO04hY93JAfnFQXgKwV.fastq.gz', '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/r6QrYNk2tYOJNCeE8OGU.jpg']