lamindb.dev.QueryManager#

class lamindb.dev.QueryManager(*args, **kwargs)#

Bases: Manager

Manage queries through fields.

See also

lamindb.dev.QuerySet django Manager

Examples

>>> ln.save(ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name"))  # noqa
>>> labels = ln.ULabel.filter(name__icontains = "label").all()
>>> ln.ULabel(name="ULabel1").save()
>>> label = ln.ULabel.filter(name="ULabel1").one()
>>> label.parents.set(labels)
>>> manager = label.parents
>>> manager.df()

Attributes

auto_created bool#

creation_counter int#

db property#

use_in_migrations bool#: If set to True the manager will be serialized into migrations and will thus be available in e.g. RunPython operations.

Methods

all()#

Return QuerySet of all.

For **kwargs, see lamindb.dev.QuerySet.df().

df(**kwargs)#

Convert to DataFrame.

For **kwargs, see lamindb.dev.QuerySet.df().

list(field=None)#

Populate a list with the results.

Examples

>>> ln.save(ln.ULabel.from_values(["ULabel1", "ULabel2", "ULabel3"], field="name"))
>>> labels = ln.ULabel.filter(name__icontains = "label").all()
>>> ln.ULabel(name="ULabel1").save()
>>> label = ln.ULabel.filter(name="ULabel1").one()
>>> label.parents.set(labels)
>>> label.parents.list()
[ULabel(id=sFMcPepC, name=ULabel1, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
ULabel(id=2SscQvsM, name=ULabel2, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse), # noqa
ULabel(id=lecV87vi, name=ULabel3, updated_at=2023-07-19 19:45:17, created_by_id=DzTjkKse)] # noqa
>>> label.parents.list("name")
['ULabel1', 'ULabel2', 'ULabel3']

lookup(field=None, **kwargs)#

Return an auto-complete object for a field.

Parameters:

field (Optional[TypeVar(StrField, str, DeferredAttribute)], default: None) – The field to look up the values for. Defaults to first string field.
return_field – The field to return. If None, returns the whole record.

Return type:

NamedTuple

Returns:

A NamedTuple of lookup information of the field values with a dictionary converter.

See also

search()

Examples

>>> import lnschema_bionty as lb
>>> lb.settings.organism = "human"
>>> lb.Gene.from_bionty(symbol="ADGB-DT").save()
>>> lookup = lb.Gene.lookup()
>>> lookup.adgb_dt
>>> lookup_dict = lookup.dict()
>>> lookup_dict['ADGB-DT']
>>> lookup_by_ensembl_id = lb.Gene.lookup(field="ensembl_gene_id")
>>> genes.ensg00000002745
>>> lookup_return_symbols = lb.Gene.lookup(field="ensembl_gene_id", return_field="symbol")

search(string, **kwargs)#

Search.

Makes reasonable choices of which fields to search.

For instance, for File, searches key and description fields.

Parameters:

string (str) – The input string to match against the field ontology values.
field – The field against which the input string is matching.
limit – Maximum amount of top results to return.
return_queryset – Return search result as a sorted QuerySet.
case_sensitive – Whether the match is case sensitive.
synonyms_field – Search synonyms if column is available. If None, is ignored.

Returns:

A sorted DataFrame of search results with a score in column score. If return_queryset is True, an ordered QuerySet.