Query & search registries¶
Find & access data using registries.
Setup¶
!lamin init --storage ./mydata
Show code cell output
💡 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 'TZGQ170jpeXkHXunNt1l' at '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/TZGQ170jpeXkHXunNt1l.jpg'
❗ no run & transform get linked, consider calling ln.track()
✅ storing artifact '0NwklWkatyxLfpYSvO4t' at '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/0NwklWkatyxLfpYSvO4t.parquet'
❗ no run & transform get linked, consider calling ln.track()
✅ storing artifact '7rDGkS54txUxBipiOLJC' at '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/7rDGkS54txUxBipiOLJC.fastq.gz'
Artifact(uid='7rDGkS54txUxBipiOLJC', description='My fastq', suffix='.fastq.gz', size=20, hash='hi7ZmAzz8sfMd3vIQr-57Q', hash_type='md5', visibility=1, key_is_virtual=True, created_by_id=1, storage_id=1, updated_at='2024-06-05 14:28:02 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='2024-06-05 14:28:00 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 | 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 | TZGQ170jpeXkHXunNt1l | None | My image | None | .jpg | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.507514+00:00 |
| 2 | 0NwklWkatyxLfpYSvO4t | None | The iris collection | None | .parquet | DataFrame | 5629 | ah24lV9Ncc8nPL0MumEsdw | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.753244+00:00 |
| 3 | 7rDGkS54txUxBipiOLJC | None | My fastq | None | .fastq.gz | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.761562+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 | 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 | 0NwklWkatyxLfpYSvO4t | None | The iris collection | None | .parquet | DataFrame | 5629 | ah24lV9Ncc8nPL0MumEsdw | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.753244+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 | ||||||||||||
| 8 | qzl9yrgfMmgjUQhj | None | Magnocellular Neurosecretory Cells Intermediat... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.757826+00:00 |
| 21 | RFoGl2O58eel0slw | None | Study study intestine IgG3 Ovaries. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.759901+00:00 |
| 25 | ie2EcifpmLycfIJy | None | Spleen intestine IgG result classify Intermedi... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.760542+00:00 |
| 27 | xF2t1fXIQeBA9afH | None | Igg Magnocellular neurosecretory cells candida... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.760864+00:00 |
| 29 | ySSSGJmTROz3Md5t | None | Intestine Uterus IgY result IgG1 IgG3. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.761177+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 | 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 | 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 | TZGQ170jpeXkHXunNt1l | None | My image | None | .jpg | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.507514+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 | 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 | 0NwklWkatyxLfpYSvO4t | None | The iris collection | None | .parquet | DataFrame | 5629 | ah24lV9Ncc8nPL0MumEsdw | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.753244+00:00 |
| 3 | 7rDGkS54txUxBipiOLJC | None | My fastq | None | .fastq.gz | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.761562+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 | 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 | TZGQ170jpeXkHXunNt1l | None | My image | None | .jpg | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.507514+00:00 |
| 3 | 7rDGkS54txUxBipiOLJC | None | My fastq | None | .fastq.gz | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.761562+00:00 |
in¶
ln.Artifact.filter(suffix__in=[".jpg", ".fastq.gz"]).df()
| uid | version | description | key | suffix | 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 | TZGQ170jpeXkHXunNt1l | None | My image | None | .jpg | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.507514+00:00 |
| 3 | 7rDGkS54txUxBipiOLJC | None | My fastq | None | .fastq.gz | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.761562+00:00 |
order by¶
ln.Artifact.filter().order_by("-updated_at").df()
| uid | version | description | key | suffix | 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 | 7rDGkS54txUxBipiOLJC | None | My fastq | None | .fastq.gz | None | 20 | hi7ZmAzz8sfMd3vIQr-57Q | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.761562+00:00 |
| 2 | 0NwklWkatyxLfpYSvO4t | None | The iris collection | None | .parquet | DataFrame | 5629 | ah24lV9Ncc8nPL0MumEsdw | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.753244+00:00 |
| 1 | TZGQ170jpeXkHXunNt1l | None | My image | None | .jpg | None | 29358 | r4tnqmKI_SjrkdLzpuWp4g | md5 | None | None | 1 | True | 1 | None | None | 1 | 2024-06-05 14:28:02.507514+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 | ||||||||||||
| 2 | 2IO07Gr0aq27NjLn | None | Igg1 research IgY IgG4 Ovaries IgG IgG. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.756872+00:00 |
| 7 | aTeLoHFRc5YfVOAR | None | Research IgY IgY Intermediate skeletal muscle ... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.757666+00:00 |
| 22 | gP53YYnGuGugBPlN | None | Research IgG3 Eardrum visualize IgG4 investigate. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.760056+00:00 |
| 24 | yssZTFObUztpUoRg | None | Igy IgG2 IgY Eosinophil granulocyte Intermedia... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.760371+00:00 |
| 31 | m2IT49uor6KQ9x4l | None | Igg4 study research IgG candidate Eardrum Huxl... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.761488+00:00 |
| 35 | GKo3JmhRM8KgnjqO | None | Intestinal IgG IgM research. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.762108+00:00 |
| 37 | W4lm5B7WAwxgTGqM | None | Igg result Spleen research IgG3 IgG3. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.762419+00:00 |
| 50 | xlUfad82sY5Mt0A2 | None | Eosinophil Granulocyte IgG Eosinophil granuloc... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.764443+00:00 |
| 54 | Ly1MoYqxID74Orev | None | Igg3 Border cells of organ of Corti investigat... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.765087+00:00 |
| 55 | G9CkoeKBvSmIF2uq | None | Uterus IgG1 IgG4 Ovaries research cluster Uter... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.765240+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 | ||||||||||||
| 2 | 2IO07Gr0aq27NjLn | None | Igg1 research IgY IgG4 Ovaries IgG IgG. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.756872+00:00 |
| 7 | aTeLoHFRc5YfVOAR | None | Research IgY IgY Intermediate skeletal muscle ... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.757666+00:00 |
| 22 | gP53YYnGuGugBPlN | None | Research IgG3 Eardrum visualize IgG4 investigate. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.760056+00:00 |
| 24 | yssZTFObUztpUoRg | None | Igy IgG2 IgY Eosinophil granulocyte Intermedia... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.760371+00:00 |
| 31 | m2IT49uor6KQ9x4l | None | Igg4 study research IgG candidate Eardrum Huxl... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.761488+00:00 |
| 35 | GKo3JmhRM8KgnjqO | None | Intestinal IgG IgM research. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.762108+00:00 |
| 37 | W4lm5B7WAwxgTGqM | None | Igg result Spleen research IgG3 IgG3. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.762419+00:00 |
| 50 | xlUfad82sY5Mt0A2 | None | Eosinophil Granulocyte IgG Eosinophil granuloc... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.764443+00:00 |
| 54 | Ly1MoYqxID74Orev | None | Igg3 Border cells of organ of Corti investigat... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.765087+00:00 |
| 55 | G9CkoeKBvSmIF2uq | None | Uterus IgG1 IgG4 Ovaries research cluster Uter... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.765240+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 | ||||||||||||
| 7 | aTeLoHFRc5YfVOAR | None | Research IgY IgY Intermediate skeletal muscle ... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.757666+00:00 |
| 22 | gP53YYnGuGugBPlN | None | Research IgG3 Eardrum visualize IgG4 investigate. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.760056+00:00 |
| 67 | Uyj0wBLvGQB2Ca52 | None | Research IgG3 Eosinophil granulocyte IgG Natur... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.767085+00:00 |
| 153 | MV3y64z9RoJWAl7s | None | Research IgY IgG1 Uterus. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.786865+00:00 |
| 204 | 4u8GAoZdORRJGULW | None | Research Astrocytes Astrocytes IgY. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.794636+00:00 |
| 222 | 7TDj7IQPYUyURwoC | None | Research IgG3 Lymph node Liver IgY. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.797349+00:00 |
| 255 | msNk0NMGoTpidqez | None | Research classify IgG1 IgG1 Natural killer T c... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.805008+00:00 |
| 310 | Z468gP8ye3WZb4Jh | None | Research Uterus Liver Uterus IgG research IgG4. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.816080+00:00 |
| 324 | WTssze8FTr4fPeLe | None | Research IgG1 Huxley's layer IgG. | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.818192+00:00 |
| 380 | 1ao0DUkCecjo9d2L | None | Research IgY Huxley's layer Magnocellular neur... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.826599+00:00 |
| 406 | Ps9oX8BwMiRwiVIZ | None | Research IgG IgG Border cells of organ of Cort... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.833312+00:00 |
| 408 | W8NsDI1m8hv4brKE | None | Research IgG4 Border cells of organ of Corti I... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.833608+00:00 |
| 485 | S8zDuuPaXRzHeHUd | None | Research IgE Liver efficiency Lymph node resea... | None | None | notebook | None | None | None | None | 1 | 2024-06-05 14:28:07.847991+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/0NwklWkatyxLfpYSvO4t.parquet', '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/7rDGkS54txUxBipiOLJC.fastq.gz', '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/TZGQ170jpeXkHXunNt1l.jpg', '/home/runner/work/lamindb/lamindb/docs/mydata/.lamindb/_is_initialized']