src.features.smarterdb

Created on Tue Feb 23 16:21:35 2021

@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>

Classes:

`Breed`(args, *values)
`BreedAlias`(args, *kwargs)	Required to describe the breed and code used in a certain dataset in order to resolve the final breed to be used in SMARTER-database
`Consequence`(args, *kwargs)	A class to manage SNP consequences.
`Counter`(args, *values)	A class to deal with counter collection (created when initializing smarter database) and used to define SMARTER IDs
`Country`([name])	A helper class to deal with countries object.
`Dataset`(args, *values)	Describe a dataset instace with fields owned by data types
`Location`(args, *kwargs)	A class to deal with a SNP location (ie position in an assembly for a certain chip or data source)
`Phenotype`(args, *kwargs)	A class to deal with phenotypes.
`Probeset`(args, *kwargs)	A class to deal with different affymetrix probesets
`SAMPLETYPE`(value)	A simple Enum object to define sample type (`background` or `foreground`)
`SEX`(value)	An enum object to manage Sample sex in the same way as plink does
`SampleGoat`(args, *values)	A class specific for Goat samples
`SampleSheep`(args, *values)	A class specific for Sheep samples
`SampleSpecies`(args, *values)	A generic class used to manage Goat or Sheep samples
`SmarterInfo`(args, *values)	A class to track database status informations
`SupportedChip`(args, *values)	A class to deal with SMARTER-database managed chips
`VariantGoat`(args, *values)	A class to deal with Goat variations (SNP)
`VariantSheep`(args, *values)	A class to deal with Sheep variations (SNP)
`VariantSpecies`(args, *values)	Generic class to deal with Variant (SNP) objects

Exceptions:

SmarterDBException

Functions:

`complement`(genotype)	Return reverse complement for a base call
`getNextSequenceValue`(sequence_name, mongodb)	Read from `Counter` collection and determine the next sequence number to be used for the SMARTER ID
`getSmarterId`(species_class, country, breed)	Generate a new SMARTER ID object using the internal counter collections
`get_or_create_breed`(species_class, name, code)	Get a Breed instance or create a new one (or update a breed adding a new `BreedAlias`)
`get_or_create_sample`(SampleSpecies, ...[, ...])	Get or create a sample providing attributes (search for original_id in provided dataset
`get_sample_type`(dataset)	test if foreground or background dataset
`global_connection`([database_name])	Establish a connection to the SMARTER database.

class src.features.smarterdb.Breed(*args, **values)[source]

Bases: Document

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`aliases`	A list of `BreedAlias` objects.
`code`	The breed code
`id`	A field wrapper around MongoDB's ObjectIds.
`n_individuals`	How many samples are the same breed
`name`	The breed name
`objects`([q_obj])
`species`	The breed species.

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

aliases: A list of BreedAlias objects. Required to determine the SMARTER-database breed from the genotype file (which can use a different breed name or code)

code: The breed code

id: A field wrapper around MongoDB’s ObjectIds.

n_individuals: How many samples are the same breed

name: The breed name

objects(q_obj=None, **query) = []

species: The breed species. Should be one of Goat or Sheep

class src.features.smarterdb.BreedAlias(*args, **kwargs)[source]

Bases: EmbeddedDocument

Required to describe the breed and code used in a certain dataset in order to resolve the final breed to be used in SMARTER-database

Attributes:

`country`	The country of the breed in the dataset.
`dataset`	The dataset `ObjectID` in which this BreedAlias is used
`fid`	The breed Family ID used in genotype file

country: The country of the breed in the dataset. Used in multi country datasets

dataset: The dataset ObjectID in which this BreedAlias is used

fid: The breed Family ID used in genotype file

class src.features.smarterdb.Consequence(*args, **kwargs)[source]

Bases: EmbeddedDocument

A class to manage SNP consequences. Not yet implemented

class src.features.smarterdb.Counter(*args, **values)[source]

Bases: Document

A class to deal with counter collection (created when initializing smarter database) and used to define SMARTER IDs

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`id`	A unicode string field.
`objects`([q_obj])
`sequence_value`	32-bit integer field.

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

id: A unicode string field.

objects(q_obj=None, **query) = []

sequence_value: 32-bit integer field.

class src.features.smarterdb.Country(name: Optional[str] = None, *args, **kwargs)[source]

Bases: Document

A helper class to deal with countries object. Each record is created after data import, when database status is updated

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Methods:

__init__([name])

Initialise a document or an embedded document.

Attributes:

`alpha_2`	Country 2 letter code (used to derive SMARTER IDs)
`alpha_3`	Country 3 letter code
`id`	A field wrapper around MongoDB's ObjectIds.
`name`	The Country name
`numeric`	The country numeric code
`objects`([q_obj])
`official_name`	Country ufficial name
`species`	The sample species find within this country

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

__init__(name: Optional[str] = None, *args, **kwargs)[source]

Initialise a document or an embedded document.

Parameters

values – A dictionary of keys and values for the document. It may contain additional reserved keywords, e.g. “__auto_convert”.
__auto_convert – If True, supplied values will be converted to Python-type values via each field’s to_python method.
_created – Indicates whether this is a brand new document or whether it’s already been persisted before. Defaults to true.

alpha_2: Country 2 letter code (used to derive SMARTER IDs)

alpha_3: Country 3 letter code

id: A field wrapper around MongoDB’s ObjectIds.

name: The Country name

numeric: The country numeric code

objects(q_obj=None, **query) = []

official_name: Country ufficial name

species: The sample species find within this country

class src.features.smarterdb.Dataset(*args, **values)[source]

Bases: Document

Describe a dataset instace with fields owned by data types

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`breed`	The breed of the dataset.
`chip_name`	The `SupportedChip.name` attribute of the technology used
`contents`	Dataset contents as a list
`country`	The country where the data come from.
`doi`	The publication DOI of this dataset
`file`	The source dataset file
`gene_array`	The technology used to generate data specified by the partner
`id`	A field wrapper around MongoDB's ObjectIds.
`n_of_individuals`	Number of individual in the dataset
`n_of_records`	Number of the record in the phenotype file
`objects`([q_obj])
`partner`	The partner which owns the dataset
`result_dir`	returns the locations of dataset processed directory.
`size_`	The file size
`species`	The species of the data.
`trait`	Trait described in phenotype file
`type_`	Dataset type.
`uploader`	The partner which upload this dataset
`working_dir`	returns the locations of dataset working directory.

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

breed: The breed of the dataset. Could have many values

chip_name: The SupportedChip.name attribute of the technology used

contents: Dataset contents as a list

country: The country where the data come from. Could have many values

doi: The publication DOI of this dataset

file: The source dataset file

gene_array: The technology used to generate data specified by the partner

id: A field wrapper around MongoDB’s ObjectIds.

n_of_individuals: Number of individual in the dataset

n_of_records: Number of the record in the phenotype file

objects(q_obj=None, **query) = []

partner: The partner which owns the dataset

property result_dir: PosixPath

returns the locations of dataset processed directory. Could exists or not

Returns: a subdirectory in /data/processed/
Return type: pathlib.PosixPath

size_: The file size

species: The species of the data. Could be ‘Sheep’ or ‘Goat’

trait: Trait described in phenotype file

type_: Dataset type. Need to be one from ['genotypes', 'phenotypes] and one from ['background', 'foreground']

uploader: The partner which upload this dataset

property working_dir: PosixPath

returns the locations of dataset working directory. Could exists or not

Returns: a subdirectory in /data/interim/
Return type: pathlib.PosixPath

class src.features.smarterdb.Location(*args, **kwargs)[source]

Bases: EmbeddedDocument

A class to deal with a SNP location (ie position in an assembly for a certain chip or data source)

Methods:

`__init__`(args, *kwargs)	Initialise a document or an embedded document.
`ab2top`(genotype[, missing])	Convert an illumina ab SNP in a illumina top snp
`affy2top`(genotype[, missing])	Convert an affymetrix SNP in a illumina top snp
`forward2top`(genotype[, missing])	Convert an illumina forward SNP in a illumina top snp
`illumina2top`(genotype[, missing])	Convert an illumina SNP in a illumina top snp
`is_ab`(genotype[, missing])	Return True if genotype is compatible with illumina AB coding
`is_affymetrix`(genotype[, missing])	Return True if genotype is compatible with affymetrix coding
`is_forward`(genotype[, missing])	Return True if genotype is compatible with illumina FORWARD coding
`is_illumina`(genotype[, missing])	Return True if genotype is compatible with illumina coding (as it's recorded in manifest)
`is_top`(genotype[, missing])	Return True if genotype is compatible with illumina TOP coding

Attributes:

`affymetrix_ab`	The SNP code read as it is from affymetrix data
`alleles`	The dbSNP alleles of such SNP
`chrom`	The chromosome where this SNP is located
`consequences`	A list of SNP consequences (not yet implemented)
`date`	Track manifactured date or when this data was last updated
`illumina`	The SNP code read as it is from illumina data
`illumina_forward`	The SNP code in illumina forward coding
`illumina_strand`	The probe orientation in alignment
`illumina_top`	Return genotype in illumina top format
`imported_from`	The source of the SNP data
`position`	The SNP position
`ss_id`	The SNP subission ID
`strand`	The strand orientation in aligment
`version`	The assembly version where this SNP is placed

__init__(*args, **kwargs)[source]

Initialise a document or an embedded document.

Parameters

values – A dictionary of keys and values for the document. It may contain additional reserved keywords, e.g. “__auto_convert”.
__auto_convert – If True, supplied values will be converted to Python-type values via each field’s to_python method.
_created – Indicates whether this is a brand new document or whether it’s already been persisted before. Defaults to true.

ab2top(genotype: list, missing: list = ['0', '-']) → list[source]

Convert an illumina ab SNP in a illumina top snp

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’B’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

The genotype in top format

Return type

list

affy2top(genotype: list, missing: list = ['0', '-']) → list[source]

Convert an affymetrix SNP in a illumina top snp

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’C’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

The genotype in top format

Return type

list

affymetrix_ab: The SNP code read as it is from affymetrix data

alleles: The dbSNP alleles of such SNP

chrom: The chromosome where this SNP is located

consequences: A list of SNP consequences (not yet implemented)

date: Track manifactured date or when this data was last updated

forward2top(genotype: list, missing: list = ['0', '-']) → list[source]

Convert an illumina forward SNP in a illumina top snp

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’C’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

The genotype in top format

Return type

list

illumina: The SNP code read as it is from illumina data

illumina2top(genotype: list, missing: list = ['0', '-']) → list[source]

Convert an illumina SNP in a illumina top snp

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’C’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

The genotype in top format

Return type

list

illumina_forward: The SNP code in illumina forward coding

illumina_strand: The probe orientation in alignment

property illumina_top: Return genotype in illumina top format

imported_from: The source of the SNP data

is_ab(genotype: list, missing: list = ['0', '-']) → bool[source]

Return True if genotype is compatible with illumina AB coding

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’B’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

True if in AB coding

Return type

bool

is_affymetrix(genotype: list, missing: list = ['0', '-']) → bool[source]

Return True if genotype is compatible with affymetrix coding

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’C’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

True if in affymetrix AB coding

Return type

bool

is_forward(genotype: list, missing: list = ['0', '-']) → bool[source]

Return True if genotype is compatible with illumina FORWARD coding

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’C’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

True if in forward coding

Return type

bool

is_illumina(genotype: list, missing: list = ['0', '-']) → bool[source]

Return True if genotype is compatible with illumina coding (as it’s recorded in manifest)

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’C’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

True if in affymetrix AB coding

Return type

bool

is_top(genotype: list, missing: list = ['0', '-']) → bool[source]

Return True if genotype is compatible with illumina TOP coding

Parameters

genotype (list) – a list of two alleles (ex [‘A’,’C’])
missing (list) – a list of missing allele strings (def [“0”, “-“])

Returns

True if in top coding

Return type

bool

position: The SNP position

ss_id: The SNP subission ID

strand: The strand orientation in aligment

version: The assembly version where this SNP is placed

class src.features.smarterdb.Phenotype(*args, **kwargs)[source]

Bases: DynamicEmbeddedDocument

A class to deal with phenotypes. This is a dynamic document and not a generic DictField since there can be attributes which could be enforced to have certain values. All other attributes could be set without any assumptions

Attributes:

`chest_girth`	Floating point number field.
`height`	Floating point number field.
`length`	Floating point number field.
`purpose`	A unicode string field.

chest_girth: Floating point number field.

height: Floating point number field.

length: Floating point number field.

purpose: A unicode string field.

class src.features.smarterdb.Probeset(*args, **kwargs)[source]

Bases: EmbeddedDocument

A class to deal with different affymetrix probesets

Attributes:

`chip_name`	the chip name where this affymetrix probeset comes from
`probeset_id`	A list probeset assigned to the same SNP

chip_name: the chip name where this affymetrix probeset comes from

probeset_id: A list probeset assigned to the same SNP

class src.features.smarterdb.SAMPLETYPE(value)[source]

Bases: Enum

A simple Enum object to define sample type (background or foreground)

Attributes:

`BACKGROUND`
`FOREGROUND`

BACKGROUND = 'background'

FOREGROUND = 'foreground'

class src.features.smarterdb.SEX(value)[source]

Bases: bytes, Enum

An enum object to manage Sample sex in the same way as plink does

Attributes:

`FEMALE`
`MALE`
`UNKNOWN`

Methods:

from_string(value)

Get proper type relying on input string

FEMALE = 2

MALE = 1

UNKNOWN = 0

classmethod from_string(value: str)[source]

Get proper type relying on input string

Parameters: value (str) – required sex as string
Returns: A sex instance (MALE, FEMALE, UNKNOWN)
Return type: SEX

class src.features.smarterdb.SampleGoat(*args, **values)[source]

Bases: SampleSpecies

A class specific for Goat samples

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`father_id`	The father (SIRE) of this animal.
`id`	A field wrapper around MongoDB's ObjectIds.
`mother_id`	The mother (DAM) of this animal.
`objects`([q_obj])
`species`	The species name.
`species_class`	The generic specie class

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

father_id: The father (SIRE) of this animal. Is a reference to another SampleGoat instance

id: A field wrapper around MongoDB’s ObjectIds.

mother_id: The mother (DAM) of this animal. Is a reference to another SampleGoat instance

objects(q_obj=None, **query) = []

species: The species name. Could be something different from Capra hircus

species_class = 'Goat': The generic specie class

class src.features.smarterdb.SampleSheep(*args, **values)[source]

Bases: SampleSpecies

A class specific for Sheep samples

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`father_id`	The father (SIRE) of this animal.
`id`	A field wrapper around MongoDB's ObjectIds.
`mother_id`	The mother (DAM) of this animal.
`objects`([q_obj])
`species`	The species name.
`species_class`	The generic specie class

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

father_id: The father (SIRE) of this animal. Is a reference to another SampleSheep instance

id: A field wrapper around MongoDB’s ObjectIds.

mother_id: The mother (DAM) of this animal. Is a reference to another SampleSheep instance

objects(q_obj=None, **query) = []

species: The species name. Could be something different from Ovis aries

species_class = 'Sheep': The generic specie class

class src.features.smarterdb.SampleSpecies(*args, **values)[source]

Bases: Document

A generic class used to manage Goat or Sheep samples

Attributes:

`alias`	This is a sample alias, mainly the name used in the genotype file, which can be different from the name specified in the metadata file
`breed`	The breed full name
`breed_code`	The breed code
`chip_name`	The chip name used to define this sample
`country`	Where this samples comes from
`dataset`	The dataset where this sample come from
`locations`	The sample GPS location as a Point (X, Y -> longitude, latitude).
`metadata`	Additional metadata (not managed via ORM)
`original_id`	The sample original ID in the source dataset
`phenotype`	A `Phenotype` instance
`sex`	A `SEX` instance.
`smarter_id`	A SMARTER unique and stable identifier
`species_class`	A generic species (Sheep or Goat).
`type_`	A `SAMPLETYPE` instance (ie, `background` or `foreground`

Methods:

save(*args, **kwargs)

Custom save method.

alias: This is a sample alias, mainly the name used in the genotype file, which can be different from the name specified in the metadata file

breed: The breed full name

breed_code: The breed code

chip_name: The chip name used to define this sample

country: Where this samples comes from

dataset: The dataset where this sample come from

locations: The sample GPS location as a Point (X, Y -> longitude, latitude). Mind that a location is specified in latitude and longitude coordinates. Specifying coordinates header in general is useful to avoid errors

metadata: Additional metadata (not managed via ORM)

original_id: The sample original ID in the source dataset

phenotype: A Phenotype instance

save(*args, **kwargs)[source]: Custom save method. Deal with smarter_id before save

sex: A SEX instance. Store sex like plink does

smarter_id: A SMARTER unique and stable identifier

species_class = None: A generic species (Sheep or Goat). Used to determine specific methods and to identify the proper data from the database

type_: A SAMPLETYPE instance (ie, background or foreground

exception src.features.smarterdb.SmarterDBException[source]: Bases: Exception

class src.features.smarterdb.SmarterInfo(*args, **values)[source]

Bases: Document

A class to track database status informations

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`id`	A unicode string field.
`last_updated`	When the SMARTER-database was updated for the last time
`objects`([q_obj])
`plink_specie_opt`	The plink parameters used to generate the final genotype dataset
`version`	The SMARTER-database version
`working_assemblies`	A dictionary in which managed assemblies are tracked

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

id: A unicode string field.

last_updated: When the SMARTER-database was updated for the last time

objects(q_obj=None, **query) = []

plink_specie_opt: The plink parameters used to generate the final genotype dataset

version: The SMARTER-database version

working_assemblies: A dictionary in which managed assemblies are tracked

class src.features.smarterdb.SupportedChip(*args, **values)[source]

Bases: Document

A class to deal with SMARTER-database managed chips

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`id`	A field wrapper around MongoDB's ObjectIds.
`manifacturer`	Who created the chip
`n_of_snps`	How many SNPs are described within this chip
`name`	The chip identifier
`objects`([q_obj])
`species`	The species for which a chip is defined

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

id: A field wrapper around MongoDB’s ObjectIds.

manifacturer: Who created the chip

n_of_snps: How many SNPs are described within this chip

name: The chip identifier

objects(q_obj=None, **query) = []

species: The species for which a chip is defined

class src.features.smarterdb.VariantGoat(*args, **values)[source]

Bases: VariantSpecies

A class to deal with Goat variations (SNP)

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`id`	A field wrapper around MongoDB's ObjectIds.
`objects`([q_obj])

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

id: A field wrapper around MongoDB’s ObjectIds.

objects(q_obj=None, **query) = []

class src.features.smarterdb.VariantSheep(*args, **values)[source]

Bases: VariantSpecies

A class to deal with Sheep variations (SNP)

Miscellaneous:

`DoesNotExist`
`MultipleObjectsReturned`

Attributes:

`id`	A field wrapper around MongoDB's ObjectIds.
`objects`([q_obj])

exception DoesNotExist: Bases: DoesNotExist

exception MultipleObjectsReturned: Bases: MultipleObjectsReturned

id: A field wrapper around MongoDB’s ObjectIds.

objects(q_obj=None, **query) = []

class src.features.smarterdb.VariantSpecies(*args, **values)[source]

Bases: Document

Generic class to deal with Variant (SNP) objects

Attributes:

`affy_snp_id`	The affymetrix SNP id
`chip_name`	The chip names where this SNP could be found
`cust_id`	The affymetrix customer id (which is the illumina name)
`illumina_top`	Illumina TOP variant (which is the same indipendently by locations)
`locations`	A list of `Location` objects
`name`	The name of the SNPs.
`probesets`	A list of `Probeset` objects
`rs_id`	The SNP rsID
`sender`	Who provide this SNP probe
`sequence`	A dictionary where keys are chip_name, and values are their probe sequences

Methods:

`get_location`(version[, imported_from])	Returns location for assembly version and imported source
`get_location_index`(version[, imported_from])	Returns location index for assembly version and imported source
`save`(args, *kwargs)	Custom save method.

affy_snp_id: The affymetrix SNP id

chip_name: The chip names where this SNP could be found

cust_id: The affymetrix customer id (which is the illumina name)

get_location(version: str, imported_from='SNPchiMp v.3')[source]

Returns location for assembly version and imported source

Parameters

version (str) – assembly version (ex: ‘Oar_v3.1’)
imported_from (str) – coordinates source (ex: ‘SNPchiMp v.3’)

Returns

the genomic coordinates

Return type

Location

get_location_index(version: str, imported_from='SNPchiMp v.3')[source]

Returns location index for assembly version and imported source

Parameters

version (str) – assembly version (ex: ‘Oar_v3.1’)
imported_from (str) – coordinates source (ex: ‘SNPchiMp v.3’)

Returns

the index of the location requested

Return type

int

illumina_top: Illumina TOP variant (which is the same indipendently by locations)

locations: A list of Location objects

name: The name of the SNPs. Could be illumina name or affyemtrix name

probesets: A list of Probeset objects

rs_id: The SNP rsID

save(*args, **kwargs)[source]: Custom save method. Deal with variant name before save

sender: Who provide this SNP probe

sequence: A dictionary where keys are chip_name, and values are their probe sequences

src.features.smarterdb.complement(genotype: str) → str[source]

Return reverse complement for a base call

Parameters: genotype (str) – A base call (one from A, T, G, C).
Returns: result – The reverse complement of the base call.
Return type: str

src.features.smarterdb.getNextSequenceValue(sequence_name: str, mongodb: Database)[source]: Read from Counter collection and determine the next sequence number to be used for the SMARTER ID

src.features.smarterdb.getSmarterId(species_class: str, country: str, breed: str) → str[source]

Generate a new SMARTER ID object using the internal counter collections

Parameters

species_class (str) – The class of the species (should be ‘Goat’ or ‘Sheep’).
country (str) – The country name of the sample.
breed (str) – The breed name of the sample.

Raises

SmarterDBException – Raised when passing a wrong species or no one.

Returns

A new smarter_id.

Return type

str

src.features.smarterdb.get_or_create_breed(species_class: str, name: str, code: str, aliases: list = []) → [<class 'src.features.smarterdb.Breed'>, <class 'bool'>][source]

Get a Breed instance or create a new one (or update a breed adding a new BreedAlias)

Parameters

species_class (str) – The class of the species (should be ‘Goat’ or ‘Sheep’)
name (str) – The breed full name.
code (str) – The breed code (unique in Sheep and Goats collections).
aliases (list, optional) – A list of BreedAlias objects. The default is [].

Raises

SmarterDBException – Raised if the breed is not Unique.

Returns

breed (Breed) – A Breed instance.
modified (bool) – True is breed is created (or alias updated).

src.features.smarterdb.get_or_create_sample(SampleSpecies: Union[SampleGoat, SampleSheep], original_id: str, dataset: Dataset, type_: str, breed: Breed, country: str, species: Optional[str] = None, chip_name: Optional[str] = None, sex: Optional[SEX] = None, alias: Optional[str] = None) → list[Union[src.features.smarterdb.SampleGoat, src.features.smarterdb.SampleSheep], bool][source]

Get or create a sample providing attributes (search for original_id in provided dataset

Parameters

SampleSpecies (Union[SampleGoat, SampleSheep]) – the class required for insert/update.
original_id (str) – the original_id in the dataset.
dataset (Dataset) – the dataset instance used to register sample.
type (str) – sample type. “background” or “foreground” are the only values accepted
breed (Breed) – a Breed instance.
country (str) – the country where the sample comes from.
species (str, optional) – The sample species. If None, the default species_class attribute will be used
chip_name (str, optional) – the chip name. The default is None.
sex (SEX, optional) – A SEX instance. The default is None.
alias (str, optional) – an original_id alias. Could be the name used in the genotype file, which could be different from the original_id. The default is None.

Raises

SmarterDBException – Raised multiple samples are returned (should never happen).

Returns

Union[SampleGoat, SampleSheep] – a SampleSpecies instance.
created (bool) – True is sample is created.

src.features.smarterdb.get_sample_type(dataset: Dataset)[source]

test if foreground or background dataset

Parameters: dataset (Dataset) – the dataset instance used to register sample
Returns: sample type (“background” or “foreground”)
Return type: str

src.features.smarterdb.global_connection(database_name: str = 'smarter') → MongoClient[source]

Establish a connection to the SMARTER database. Reads environment parameters using load_dotenv(), returns a MongoClient object.

Parameters: database_name (str, optional) – The smarter database. The default is ‘smarter’.
Returns: CLIENT – a mongoclient instance.
Return type: MongoClient