lamindb.Run¶
- class lamindb.Run(transform: Transform, reference: str | None = None, reference_type: str | None = None)¶
Bases:
Record
Runs of transforms.
- Parameters:
transform –
Transform
ATransform
record.reference –
str | None = None
For instance, an external ID or a download URL.reference_type –
str | None = None
For instance,redun_id
,nextflow_id
orurl
.
See also
track()
Track global run & transform records for a notebook or pipeline.
Examples
Create a run record:
>>> ln.Transform(name="Cell Ranger", version="7.2.0", type="pipeline").save() >>> transform = ln.Transform.get(name="Cell Ranger", version="7.2.0") >>> run = ln.Run(transform)
Create a global run context for a custom transform:
>>> ln.track(transform=transform) >>> ln.context.run # globally available run
Track a global run context for a notebook or script:
>>> ln.track() # Jupyter notebook metadata is automatically parsed >>> ln.context.run
Attributes¶
-
params:
ParamManager
¶ Param manager.
Guide: Track run parameters
Example:
run.params.add_values({ "learning_rate": 0.01, "input_dir": "s3://my-bucket/mydataset", "downsample": True, "preprocess_params": { "normalization_type": "cool", "subset_highlyvariable": True, }, })
Simple fields¶
-
uid:
str
¶ Universal id, valid across DB instances.
-
started_at:
datetime
¶ Start time of run.
-
finished_at:
datetime
¶ Finished time of run.
-
is_consecutive:
bool
¶ Indicates whether code was consecutively executed. Is relevant for notebooks.
-
reference:
str
¶ A reference like a URL or external ID (such as from a workflow manager).
-
reference_type:
str
¶ Type of reference such as a workflow manager execution ID.
-
created_at:
datetime
¶ Time of first creation. Mismatches
started_at
if the run is re-run.
Relational fields¶
-
environment:
Artifact
¶ Computational environment for the run.
For instance,
Dockerfile
,docker image
,requirements.txt
,environment.yml
, etc.
-
parent:
Run
¶ The run that triggered the current run.
This is not a preceding run. The preceding runs (“predecessors”) is the set of runs that produced the output artifacts that serve as the inputs for the present run.
Be careful with using this field at this point.
-
input_artifacts:
Artifact
¶ The artifacts serving as input for this run.
Related accessor:
input_of_runs
.
-
output_collections:
Collection
¶ The collections generated by this run.
-
input_collections:
Collection
¶ The collections serving as input for this run.
Class methods¶
- classmethod df(include=None, join='inner', limit=100)¶
Convert to
pd.DataFrame
.By default, shows all direct fields, except
created_at
.If you’d like to include related fields, use parameter
include
.- Parameters:
include (
str
|list
[str
] |None
, default:None
) – Related fields to include as columns. Takes strings of form"labels__name"
,"cell_types__name"
, etc. or a list of such strings.join (
str
, default:'inner'
) – Thejoin
parameter ofpandas
.
- Return type:
DataFrame
Examples
>>> labels = [ln.ULabel(name="Label {i}") for i in range(3)] >>> ln.save(labels) >>> ln.ULabel.filter().df(include=["created_by__name"])
- classmethod filter(*queries, **expressions)¶
Query records.
- Parameters:
queries – One or multiple
Q
objects.expressions – Fields and values passed as Django query expressions.
- Return type:
QuerySet
- Returns:
A
QuerySet
.
See also
Guide: Query & search registries
Django documentation: Queries
Examples
>>> ln.ULabel(name="my ulabel").save() >>> ulabel = ln.ULabel.get(name="my ulabel")
- classmethod get(idlike=None, **expressions)¶
Get a single record.
- Parameters:
idlike (
int
|str
|None
, default:None
) – Either a uid stub, uid or an integer id.expressions – Fields and values passed as Django query expressions.
- Return type:
- Returns:
A record.
- Raises:
lamindb.core.exceptions.DoesNotExist – In case no matching record is found.
See also
Guide: Query & search registries
Django documentation: Queries
Examples
>>> ulabel = ln.ULabel.get("2riu039") >>> ulabel = ln.ULabel.get(name="my-label")
- classmethod lookup(field=None, return_field=None)¶
Return an auto-complete object for a field.
- Parameters:
field (
str
|DeferredAttribute
|None
, default:None
) – The field to look up the values for. Defaults to first string field.return_field (
str
|DeferredAttribute
|None
, default:None
) – The field to return. IfNone
, returns the whole record.
- Return type:
NamedTuple
- Returns:
A
NamedTuple
of lookup information of the field values with a dictionary converter.
See also
Examples
>>> import bionty as bt >>> bt.settings.organism = "human" >>> bt.Gene.from_source(symbol="ADGB-DT").save() >>> lookup = bt.Gene.lookup() >>> lookup.adgb_dt >>> lookup_dict = lookup.dict() >>> lookup_dict['ADGB-DT'] >>> lookup_by_ensembl_id = bt.Gene.lookup(field="ensembl_gene_id") >>> genes.ensg00000002745 >>> lookup_return_symbols = bt.Gene.lookup(field="ensembl_gene_id", return_field="symbol")
- classmethod search(string, *, field=None, limit=20, case_sensitive=False)¶
Search.
- Parameters:
string (
str
) – The input string to match against the field ontology values.field (
str
|DeferredAttribute
|None
, default:None
) – The field or fields to search. Search all string fields by default.limit (
int
|None
, default:20
) – Maximum amount of top results to return.case_sensitive (
bool
, default:False
) – Whether the match is case sensitive.
- Return type:
QuerySet
- Returns:
A sorted
DataFrame
of search results with a score in columnscore
. Ifreturn_queryset
isTrue
.QuerySet
.
Examples
>>> ulabels = ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name") >>> ln.save(ulabels) >>> ln.ULabel.search("ULabel2")
- classmethod using(instance)¶
Use a non-default LaminDB instance.
- Parameters:
instance (
str
|None
) – An instance identifier of form “account_handle/instance_name”.- Return type:
QuerySet
Examples
>>> ln.ULabel.using("account_handle/instance_name").search("ULabel7", field="name") uid score name ULabel7 g7Hk9b2v 100.0 ULabel5 t4Jm6s0q 75.0 ULabel6 r2Xw8p1z 75.0
Methods¶
- delete()¶
- Return type:
None