Project flow#
LaminDB allows tracking data lineage on the entire project level.
Here, we walk through exemplified app uploads, pipelines & notebooks following Schmidt et al., 2022.
A CRISPR screen reading out a phenotypic endpoint on T cells is paired with scRNA-seq to generate insights into IFN-γ production.
These insights get linked back to the original data through the steps taken in the project to provide context for interpretation & future decision making.
More specifically: Why should I care about data flow?
Data flow tracks data sources & transformations to trace biological insights, verify experimental outcomes, meet regulatory standards, increase the robustness of research and optimize the feedback loop of team-wide learning iterations.
While tracking data flow is easier when it’s governed by deterministic pipelines, it becomes hard when it’s governed by interactive human-driven analyses.
LaminDB interfaces workflow mangers for the former and embraces the latter.
Setup#
Init a test instance:
!lamin init --storage ./mydata
Show code cell output
❗ Couldn't retrieve user id (the `created_by` field couldn't be set correctly).
Your user is not yet part of the User registry of this instance. Run
from lamindb_setup._init_instance import register_user
register_user(ln.setup.settings.user)
💡 connected lamindb: testuser1/mydata
Import lamindb:
import lamindb as ln
from IPython.display import Image, display
💡 connected lamindb: testuser1/mydata
Steps#
In the following, we walk through exemplified steps covering different types of transforms (Transform).
Note
The full notebooks are in this repository.
App upload of phenotypic data 
#
Register data through app upload from wetlab by testuser1:
# This function mimics the upload of artifacts via the UI
# In reality, you simply drag and drop files into the UI
def mock_upload_crispra_result_app():
ln.setup.login("testuser1")
transform = ln.Transform(name="Upload GWS CRISPRa result", type="upload")
ln.track(transform=transform)
output_path = ln.core.datasets.schmidt22_crispra_gws_IFNG(ln.settings.storage)
output_file = ln.Artifact(
output_path, description="Raw data of schmidt22 crispra GWS"
)
output_file.save()
mock_upload_crispra_result_app()
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💡 saved: Transform(uid='U3BxICUq8M9mLffQ', name='Upload GWS CRISPRa result', type='upload', updated_at=2024-05-06 19:36:32 UTC, created_by_id=1)
💡 saved: Run(uid='nxzMTxM2SkioaqSPeDN1', transform_id=1, created_by_id=1)
Hit identification in notebook 
#
Access, transform & register data in drylab by testuser2 in notebook hit-identification.
Show code cell content
# the following mimics the integrated analysis notebook
# In reality, you would execute inside the notebook
import nbproject_test
from pathlib import Path
cwd = Path.cwd()
nbproject_test.execute_notebooks(cwd / "project-flow-scripts/hit-identification.ipynb", write=True)
Executing notebooks in /home/runner/work/lamin-usecases/lamin-usecases/docs/project-flow-scripts/hit-identification.ipynb
Scheduled: ['hit-identification']
hit-identification
✓ (4.903s)
Total time: 4.905s
Inspect data flow:
artifact = ln.Artifact.filter(description="hits from schmidt22 crispra GWS").one()
artifact.view_lineage()
Sequencer upload 
#
Upload files from sequencer via script chromium_10x_upload.py:
!python project-flow-scripts/chromium_10x_upload.py
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💡 connected lamindb: testuser1/mydata
💡 saved: Transform(uid='qCJPkOuZAi9q5zKv', name='chromium_10x_upload.py', key='chromium_10x_upload.py', version='1', type='script', updated_at=2024-05-06 19:36:39 UTC, created_by_id=1)
💡 saved: Run(uid='qIyibGC89qP9RBVAk46g', transform_id=3, created_by_id=1)
✅ saved transform.source_code: Artifact(uid='f7d0voyMs1WwHoVXlx2D', suffix='.py', description='Source of transform qCJPkOuZAi9q5zKv', version='1', size=474, hash='o-QoKgEZGxbk5oBtcAKoWw', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-05-06 19:36:40 UTC, storage_id=1, created_by_id=1)
✅ saved run.environment: Artifact(uid='ZCTEseLh8bdbxLes7vqa', suffix='.txt', description='requirements.txt', size=3428, hash='5BDBXeBEKrLUBHIkJCZ8hg', hash_type='md5', visibility=0, key_is_virtual=True, updated_at=2024-05-06 19:36:40 UTC, storage_id=1, created_by_id=1)
scRNA-seq bioinformatics pipeline 
#
Process uploaded files using a script or workflow manager: Pipelines and obtain 3 output files in a directory filtered_feature_bc_matrix/:
!python project-flow-scripts/cellranger.py
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💡 connected lamindb: testuser1/mydata
💡 saved: Transform(uid='fzjWGa6TRub4Se93', name='Cell Ranger', version='7.2.0', type='pipeline', reference='https://www.10xgenomics.com/support/software/cell-ranger/7.2', updated_at=2024-05-06 19:36:42 UTC, created_by_id=2)
💡 saved: Run(uid='ynfWYlVlcA6DWU1eiV0H', transform_id=4, created_by_id=2)
❗ this creates one artifact per file in the directory - you might simply call ln.Artifact(dir) to get one artifact for the entire directory
!python project-flow-scripts/postprocess_cellranger.py
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💡 connected lamindb: testuser1/mydata
💡 saved: Transform(uid='YqmbO6oMXjRj65cN', name='postprocess_cellranger.py', key='postprocess_cellranger.py', version='2', type='script', updated_at=2024-05-06 19:36:44 UTC, created_by_id=2)
💡 saved: Run(uid='NuoamNpNlc9w0WwAXm5z', transform_id=5, created_by_id=2)
Inspect data flow:
output_file = ln.Artifact.filter(description="perturbseq counts").one()
output_file.view_lineage()
Integrate scRNA-seq & phenotypic data #
Integrate data in notebook integrated-analysis.
Show code cell content
# the following mimics the integrated analysis notebook
# In reality, you would execute inside the notebook
nbproject_test.execute_notebooks(cwd / "project-flow-scripts/integrated-analysis.ipynb", write=True)
Executing notebooks in /home/runner/work/lamin-usecases/lamin-usecases/docs/project-flow-scripts/integrated-analysis.ipynb
Scheduled: ['integrated-analysis']
integrated-analysis
✓ (5.258s)
Total time: 5.260s
Review results#
Let’s load one of the plots:
# track the current notebook as transform
ln.settings.transform.stem_uid = "1LCd8kco9lZU"
ln.settings.transform.version = "0"
ln.track()
💡 notebook imports: ipython==8.24.0 lamindb==0.71.0 nbproject_test==0.5.1
💡 saved: Transform(uid='1LCd8kco9lZU6K79', name='Project flow', key='project-flow', version='0', type='notebook', updated_at=2024-05-06 19:36:51 UTC, created_by_id=1)
💡 saved: Run(uid='IypcyQ0xekMgyBhhTRnZ', transform_id=7, created_by_id=1)
artifact = ln.Artifact.filter(key__contains="figures/matrixplot").one()
artifact.cache()
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PosixUPath('/home/runner/work/lamin-usecases/lamin-usecases/docs/mydata/.lamindb/Oxo4ffnnmJBaN0sMr1Dl.png')
display(Image(filename=artifact.path))
We see that the image artifact is tracked as an input of the current notebook. The input is highlighted, the notebook follows at the bottom:
artifact.view_lineage()
Alternatively, we can also look at the sequence of transforms:
transform = ln.Transform.search("Project flow", return_queryset=True).first()
transform.parents.df()
| uid | name | key | version | description | type | latest_report_id | source_code_id | reference | reference_type | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 6 | lB3IyPLQSmvt5zKv | Perform single cell analysis, integrate with C... | integrated-analysis | 1 | None | notebook | None | None | None | None | 2024-05-06 19:36:49.546043+00:00 | 2024-05-06 19:36:49.546069+00:00 | 2 |
transform.view_parents()
Understand runs#
We tracked pipeline and notebook runs through run_context, which stores a Transform and a Run record as a global context.
Artifact objects are the inputs and outputs of runs.
What if I don’t want a global context?
Sometimes, we don’t want to create a global run context but manually pass a run when creating an artifact:
run = ln.Run(transform=transform)
ln.Artifact(filepath, run=run)
When does an artifact appear as a run input?
When accessing an artifact via cache(), load() or backed(), two things happen:
The current run gets added to
artifact.input_ofThe transform of that artifact gets added as a parent of the current transform
You can then switch off auto-tracking of run inputs if you set ln.settings.track_run_inputs = False: Can I disable tracking run inputs?
You can also track run inputs on a case by case basis via is_run_input=True, e.g., here:
artifact.load(is_run_input=True)
Query by provenance#
We can query or search for the notebook that created the artifact:
transform = ln.Transform.search("GWS CRIPSRa analysis", return_queryset=True).first()
And then find all the artifacts created by that notebook:
ln.Artifact.filter(transform=transform).df()
| uid | storage_id | key | suffix | accessor | description | version | size | hash | hash_type | n_objects | n_observations | transform_id | run_id | visibility | key_is_virtual | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 2 | kyqDNLeWBggLdMhErgCS | 1 | None | .parquet | DataFrame | hits from schmidt22 crispra GWS | None | 18368 | PihzyuN-FWc-ld6ioxAuPg | md5 | None | None | 2 | 2 | 1 | True | 2024-05-06 19:36:37.727977+00:00 | 2024-05-06 19:36:37.728000+00:00 | 1 |
Which transform ingested a given artifact?
artifact = ln.Artifact.filter().first()
artifact.transform
Transform(uid='U3BxICUq8M9mLffQ', name='Upload GWS CRISPRa result', type='upload', updated_at=2024-05-06 19:36:32 UTC, created_by_id=1)
And which user?
artifact.created_by
User(uid='DzTjkKse', handle='testuser1', name='Test User1', updated_at=2024-05-06 19:36:39 UTC)
Which transforms were created by a given user?
users = ln.User.lookup()
ln.Transform.filter(created_by=users.testuser1).df()
| uid | name | key | version | description | type | latest_report_id | source_code_id | reference | reference_type | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 1 | U3BxICUq8M9mLffQ | Upload GWS CRISPRa result | None | None | None | upload | None | NaN | None | None | 2024-05-06 19:36:32.516837+00:00 | 2024-05-06 19:36:32.516857+00:00 | 1 |
| 2 | T0T28btuB0PG5zKv | GWS CRIPSRa analysis | hit-identification | 1 | None | notebook | None | NaN | None | None | 2024-05-06 19:36:37.223874+00:00 | 2024-05-06 19:36:37.223905+00:00 | 1 |
| 3 | qCJPkOuZAi9q5zKv | chromium_10x_upload.py | chromium_10x_upload.py | 1 | None | script | None | 5.0 | None | None | 2024-05-06 19:36:39.968241+00:00 | 2024-05-06 19:36:40.432174+00:00 | 1 |
| 7 | 1LCd8kco9lZU6K79 | Project flow | project-flow | 0 | None | notebook | None | NaN | None | None | 2024-05-06 19:36:51.397451+00:00 | 2024-05-06 19:36:51.397479+00:00 | 1 |
Which notebooks were created by a given user?
ln.Transform.filter(created_by=users.testuser1, type="notebook").df()
| uid | name | key | version | description | type | latest_report_id | source_code_id | reference | reference_type | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 2 | T0T28btuB0PG5zKv | GWS CRIPSRa analysis | hit-identification | 1 | None | notebook | None | None | None | None | 2024-05-06 19:36:37.223874+00:00 | 2024-05-06 19:36:37.223905+00:00 | 1 |
| 7 | 1LCd8kco9lZU6K79 | Project flow | project-flow | 0 | None | notebook | None | None | None | None | 2024-05-06 19:36:51.397451+00:00 | 2024-05-06 19:36:51.397479+00:00 | 1 |
We can also view all recent additions to the entire database:
ln.view()
Show code cell output
Artifact
| uid | storage_id | key | suffix | accessor | description | version | size | hash | hash_type | n_objects | n_observations | transform_id | run_id | visibility | key_is_virtual | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||||||||
| 12 | Oxo4ffnnmJBaN0sMr1Dl | 1 | figures/matrixplot_fig2_score-wgs-hits-per-clu... | .png | None | None | None | 28814 | 8zXF_cVwaZnfhmrLbt_0kA | md5 | None | None | 6 | 6 | 1 | True | 2024-05-06 19:36:50.518649+00:00 | 2024-05-06 19:36:50.518673+00:00 | 2 |
| 11 | H8SlMyCsAhbaT1fNNacD | 1 | figures/umap_fig1_score-wgs-hits.png | .png | None | None | None | 118999 | DCFDLUMF-UohaBvkThn0mA | md5 | None | None | 6 | 6 | 1 | True | 2024-05-06 19:36:50.287520+00:00 | 2024-05-06 19:36:50.287542+00:00 | 2 |
| 10 | RMopT6nRcVq2PVzA3XWH | 1 | schmidt22_perturbseq.h5ad | .h5ad | AnnData | perturbseq counts | None | 20659936 | la7EvqEUMDlug9-rpw-udA | md5 | None | None | 5 | 5 | 1 | False | 2024-05-06 19:36:45.500242+00:00 | 2024-05-06 19:36:45.500272+00:00 | 2 |
| 9 | MqbLgE3gGj1rM4ZVhaCb | 1 | perturbseq/filtered_feature_bc_matrix/matrix.m... | .mtx.gz | None | None | None | 6 | oPHuNdnN6djTJBYSmAVwdA | md5 | None | None | 4 | 4 | 1 | False | 2024-05-06 19:36:42.789626+00:00 | 2024-05-06 19:36:42.789643+00:00 | 2 |
| 8 | 6nNcfDhKxtunu8njPJvD | 1 | perturbseq/filtered_feature_bc_matrix/features... | .tsv.gz | None | None | None | 6 | 1A6iSymE-MPv41hbmGsSIw | md5 | None | None | 4 | 4 | 1 | False | 2024-05-06 19:36:42.789066+00:00 | 2024-05-06 19:36:42.789084+00:00 | 2 |
| 7 | gMo2Gn9bLMDT2McN7Uj7 | 1 | perturbseq/filtered_feature_bc_matrix/barcodes... | .tsv.gz | None | None | None | 6 | X8gp1Xta1dIJ_Qr9NDS8jg | md5 | None | None | 4 | 4 | 1 | False | 2024-05-06 19:36:42.788302+00:00 | 2024-05-06 19:36:42.788321+00:00 | 2 |
| 4 | YxQ6AgD8G6VEEn8LUMp4 | 1 | fastq/perturbseq_R2_001.fastq.gz | .fastq.gz | None | None | None | 6 | kBf8igIjtkMBCbEYDqrNSQ | md5 | None | None | 3 | 3 | 1 | False | 2024-05-06 19:36:40.415484+00:00 | 2024-05-06 19:36:40.415504+00:00 | 1 |
Run
| uid | transform_id | started_at | finished_at | created_by_id | json | report_id | environment_id | is_consecutive | reference | reference_type | created_at | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | ||||||||||||
| 1 | nxzMTxM2SkioaqSPeDN1 | 1 | 2024-05-06 19:36:32.520214+00:00 | NaT | 1 | None | None | NaN | True | None | None | 2024-05-06 19:36:32.520321+00:00 |
| 2 | p4yInLO3G4hdYE9LEZEO | 2 | 2024-05-06 19:36:37.229487+00:00 | NaT | 1 | None | None | NaN | True | None | None | 2024-05-06 19:36:37.229583+00:00 |
| 3 | qIyibGC89qP9RBVAk46g | 3 | 2024-05-06 19:36:39.970826+00:00 | 2024-05-06 19:36:40.429317+00:00 | 1 | None | None | 6.0 | True | None | None | 2024-05-06 19:36:39.970957+00:00 |
| 4 | ynfWYlVlcA6DWU1eiV0H | 4 | 2024-05-06 19:36:42.332821+00:00 | NaT | 2 | None | None | NaN | None | None | None | 2024-05-06 19:36:42.332918+00:00 |
| 5 | NuoamNpNlc9w0WwAXm5z | 5 | 2024-05-06 19:36:44.376128+00:00 | NaT | 2 | None | None | NaN | None | None | None | 2024-05-06 19:36:44.376223+00:00 |
| 6 | dZCax0yTIbFHXFJOf7ms | 6 | 2024-05-06 19:36:49.554311+00:00 | NaT | 2 | None | None | NaN | True | None | None | 2024-05-06 19:36:49.554403+00:00 |
| 7 | IypcyQ0xekMgyBhhTRnZ | 7 | 2024-05-06 19:36:51.402673+00:00 | NaT | 1 | None | None | NaN | True | None | None | 2024-05-06 19:36:51.402783+00:00 |
Storage
| uid | root | description | type | region | instance_uid | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||
| 1 | aanPpD41cJZb | /home/runner/work/lamin-usecases/lamin-usecase... | None | local | None | 54ZGqgkROOFf | 2024-05-06 19:36:30.854420+00:00 | 2024-05-06 19:36:30.854438+00:00 | 1 |
Transform
| uid | name | key | version | description | type | latest_report_id | source_code_id | reference | reference_type | created_at | updated_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| id | |||||||||||||
| 7 | 1LCd8kco9lZU6K79 | Project flow | project-flow | 0 | None | notebook | None | NaN | None | None | 2024-05-06 19:36:51.397451+00:00 | 2024-05-06 19:36:51.397479+00:00 | 1 |
| 6 | lB3IyPLQSmvt5zKv | Perform single cell analysis, integrate with C... | integrated-analysis | 1 | None | notebook | None | NaN | None | None | 2024-05-06 19:36:49.546043+00:00 | 2024-05-06 19:36:49.546069+00:00 | 2 |
| 5 | YqmbO6oMXjRj65cN | postprocess_cellranger.py | postprocess_cellranger.py | 2 | None | script | None | NaN | None | None | 2024-05-06 19:36:44.373592+00:00 | 2024-05-06 19:36:44.373623+00:00 | 2 |
| 4 | fzjWGa6TRub4Se93 | Cell Ranger | None | 7.2.0 | None | pipeline | None | NaN | https://www.10xgenomics.com/support/software/c... | None | 2024-05-06 19:36:42.330453+00:00 | 2024-05-06 19:36:42.330474+00:00 | 2 |
| 3 | qCJPkOuZAi9q5zKv | chromium_10x_upload.py | chromium_10x_upload.py | 1 | None | script | None | 5.0 | None | None | 2024-05-06 19:36:39.968241+00:00 | 2024-05-06 19:36:40.432174+00:00 | 1 |
| 2 | T0T28btuB0PG5zKv | GWS CRIPSRa analysis | hit-identification | 1 | None | notebook | None | NaN | None | None | 2024-05-06 19:36:37.223874+00:00 | 2024-05-06 19:36:37.223905+00:00 | 1 |
| 1 | U3BxICUq8M9mLffQ | Upload GWS CRISPRa result | None | None | None | upload | None | NaN | None | None | 2024-05-06 19:36:32.516837+00:00 | 2024-05-06 19:36:32.516857+00:00 | 1 |
User
| uid | handle | name | created_at | updated_at | |
|---|---|---|---|---|---|
| id | |||||
| 2 | bKeW4T6E | testuser2 | Test User2 | 2024-05-06 19:36:42.320228+00:00 | 2024-05-06 19:36:42.320266+00:00 |
| 1 | DzTjkKse | testuser1 | Test User1 | 2024-05-06 19:36:30.851332+00:00 | 2024-05-06 19:36:39.836831+00:00 |
Show code cell content
!lamin login testuser1
!lamin delete --force mydata
!rm -r ./mydata
✅ logged in with email testuser1@lamin.ai (uid: DzTjkKse)
Traceback (most recent call last):
File "/opt/hostedtoolcache/Python/3.10.14/x64/bin/lamin", line 8, in <module>
sys.exit(main())
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 360, in __call__
return super().__call__(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/rich_click/rich_command.py", line 152, in main
rv = self.invoke(ctx)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamin_cli/__main__.py", line 103, in delete
return delete(instance, force=force)
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/_delete.py", line 137, in delete
n_objects = check_storage_is_empty(
File "/opt/hostedtoolcache/Python/3.10.14/x64/lib/python3.10/site-packages/lamindb_setup/core/upath.py", line 824, in check_storage_is_empty
raise InstanceNotEmpty(message)
lamindb_setup.core.upath.InstanceNotEmpty: Storage /home/runner/work/lamin-usecases/lamin-usecases/docs/mydata/.lamindb contains 5 objects ('_is_initialized' ignored) - delete them prior to deleting the instance
['/home/runner/work/lamin-usecases/lamin-usecases/docs/mydata/.lamindb/H8SlMyCsAhbaT1fNNacD.png', '/home/runner/work/lamin-usecases/lamin-usecases/docs/mydata/.lamindb/Oxo4ffnnmJBaN0sMr1Dl.png', '/home/runner/work/lamin-usecases/lamin-usecases/docs/mydata/.lamindb/ZCTEseLh8bdbxLes7vqa.txt', '/home/runner/work/lamin-usecases/lamin-usecases/docs/mydata/.lamindb/_is_initialized', '/home/runner/work/lamin-usecases/lamin-usecases/docs/mydata/.lamindb/f7d0voyMs1WwHoVXlx2D.py', '/home/runner/work/lamin-usecases/lamin-usecases/docs/mydata/.lamindb/kyqDNLeWBggLdMhErgCS.parquet']