db¶

class BaseModel(*args, **kwargs)[source]¶

Bases: peewee.Model

DoesNotExist¶: alias of BaseModelDoesNotExist

id = <AutoField: BaseModel.id>¶

class BeaconCounts(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of BeaconCountsDoesNotExist

callcount = <IntegerField: BeaconCounts.callcount>¶

datasetid = <CharField: BeaconCounts.datasetid>¶

variantcount = <IntegerField: BeaconCounts.variantcount>¶

class Collection(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

A collection is a source of data which can be sampled into a SampleSet.

DoesNotExist¶: alias of CollectionDoesNotExist

ethnicity = <CharField: Collection.ethnicity>¶

id = <AutoField: Collection.id>¶

name = <CharField: Collection.name>¶

sample_sets¶

class Coverage(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

Coverage statistics are pre-calculated for each variant for a given dataset.

The fields show the fraction of a population that reaches the mapping coverages given by the variable names.

ex. cov20 = 0.994 means that 99.4% of the population had at a mapping: coverage of at least 20 in this position.

DoesNotExist¶: alias of CoverageDoesNotExist

chrom = <CharField: Coverage.chrom>¶

coverage = <ArrayField: Coverage.coverage>¶

dataset_version = <ForeignKeyField: Coverage.dataset_version>¶

dataset_version_id = <ForeignKeyField: Coverage.dataset_version>¶

id = <AutoField: Coverage.id>¶

mean = <FloatField: Coverage.mean>¶

median = <FloatField: Coverage.median>¶

pos = <IntegerField: Coverage.pos>¶

class Dataset(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

A dataset is part of a study, and usually include a certain population.

Most studies only have a single dataset, but multiple are allowed.

DoesNotExist¶: alias of DatasetDoesNotExist

access¶

access_current¶

access_logs¶

access_pending¶

avg_seq_depth = <FloatField: Dataset.avg_seq_depth>¶

beacon_uri = <CharField: Dataset.beacon_uri>¶

browser_uri = <CharField: Dataset.browser_uri>¶

current_version¶

dataset_size = <IntegerField: Dataset.dataset_size>¶

description = <TextField: Dataset.description>¶

full_name = <CharField: Dataset.full_name>¶

has_image()[source]¶

id = <AutoField: Dataset.id>¶

logo¶

sample_sets¶

seq_center = <CharField: Dataset.seq_center>¶

seq_tech = <CharField: Dataset.seq_tech>¶

seq_type = <CharField: Dataset.seq_type>¶

short_name = <CharField: Dataset.short_name>¶

study = <ForeignKeyField: Dataset.study>¶

study_id = <ForeignKeyField: Dataset.study>¶

versions¶

class DatasetAccess(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of DatasetAccessDoesNotExist

dataset = <ForeignKeyField: DatasetAccess.dataset>¶

dataset_id = <ForeignKeyField: DatasetAccess.dataset>¶

id = <AutoField: DatasetAccess.id>¶

is_admin = <BooleanField: DatasetAccess.is_admin>¶

user = <ForeignKeyField: DatasetAccess.user>¶

user_id = <ForeignKeyField: DatasetAccess.user>¶

wants_newsletter = <BooleanField: DatasetAccess.wants_newsletter>¶

class DatasetAccessCurrent(*args, **kwargs)[source]¶

Bases: backend.db.DatasetAccess

DoesNotExist¶: alias of DatasetAccessCurrentDoesNotExist

access_requested = <DateTimeField: DatasetAccessCurrent.access_requested>¶

dataset = <ForeignKeyField: DatasetAccessCurrent.dataset>¶

dataset_id = <ForeignKeyField: DatasetAccessCurrent.dataset>¶

has_access = <IntegerField: DatasetAccessCurrent.has_access>¶

id = <AutoField: DatasetAccessCurrent.id>¶

is_admin = <BooleanField: DatasetAccessCurrent.is_admin>¶

user = <ForeignKeyField: DatasetAccessCurrent.user>¶

user_id = <ForeignKeyField: DatasetAccessCurrent.user>¶

wants_newsletter = <BooleanField: DatasetAccessCurrent.wants_newsletter>¶

class DatasetAccessPending(*args, **kwargs)[source]¶

Bases: backend.db.DatasetAccess

DoesNotExist¶: alias of DatasetAccessPendingDoesNotExist

access_requested = <DateTimeField: DatasetAccessPending.access_requested>¶

dataset = <ForeignKeyField: DatasetAccessPending.dataset>¶

dataset_id = <ForeignKeyField: DatasetAccessPending.dataset>¶

has_access = <IntegerField: DatasetAccessPending.has_access>¶

id = <AutoField: DatasetAccessPending.id>¶

is_admin = <BooleanField: DatasetAccessPending.is_admin>¶

user = <ForeignKeyField: DatasetAccessPending.user>¶

user_id = <ForeignKeyField: DatasetAccessPending.user>¶

wants_newsletter = <BooleanField: DatasetAccessPending.wants_newsletter>¶

class DatasetFile(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of DatasetFileDoesNotExist

dataset_version = <ForeignKeyField: DatasetFile.dataset_version>¶

dataset_version_id = <ForeignKeyField: DatasetFile.dataset_version>¶

download_logs¶

file_size = <IntegerField: DatasetFile.file_size>¶

id = <AutoField: DatasetFile.id>¶

name = <CharField: DatasetFile.name>¶

uri = <CharField: DatasetFile.uri>¶

class DatasetLogo(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of DatasetLogoDoesNotExist

data = <BlobField: DatasetLogo.data>¶

dataset = <ForeignKeyField: DatasetLogo.dataset>¶

dataset_id = <ForeignKeyField: DatasetLogo.dataset>¶

id = <AutoField: DatasetLogo.id>¶

mimetype = <CharField: DatasetLogo.mimetype>¶

class DatasetVersion(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of DatasetVersionDoesNotExist

available_from = <DateTimeField: DatasetVersion.available_from>¶

beacon_access = <EnumField: DatasetVersion.beacon_access>¶

consent_logs¶

coverage_levels = <ArrayField: DatasetVersion.coverage_levels>¶

coverage_set¶

data_contact_link = <CharField: DatasetVersion.data_contact_link>¶

data_contact_name = <CharField: DatasetVersion.data_contact_name>¶

dataset = <ForeignKeyField: DatasetVersion.dataset>¶

dataset_id = <ForeignKeyField: DatasetVersion.dataset>¶

description = <TextField: DatasetVersion.description>¶

file_access = <EnumField: DatasetVersion.file_access>¶

files¶

id = <AutoField: DatasetVersion.id>¶

link_hashes¶

mate¶

metrics_set¶

num_variants = <IntegerField: DatasetVersion.num_variants>¶

portal_avail = <BooleanField: DatasetVersion.portal_avail>¶

ref_doi = <CharField: DatasetVersion.ref_doi>¶

reference_set = <ForeignKeyField: DatasetVersion.reference_set>¶

reference_set_id = <ForeignKeyField: DatasetVersion.reference_set>¶

terms = <TextField: DatasetVersion.terms>¶

variants¶

version = <CharField: DatasetVersion.version>¶

class DatasetVersionCurrent(*args, **kwargs)[source]¶

Bases: backend.db.DatasetVersion

DoesNotExist¶: alias of DatasetVersionCurrentDoesNotExist

available_from = <DateTimeField: DatasetVersionCurrent.available_from>¶

beacon_access = <EnumField: DatasetVersionCurrent.beacon_access>¶

coverage_levels = <ArrayField: DatasetVersionCurrent.coverage_levels>¶

data_contact_link = <CharField: DatasetVersionCurrent.data_contact_link>¶

data_contact_name = <CharField: DatasetVersionCurrent.data_contact_name>¶

dataset = <ForeignKeyField: DatasetVersionCurrent.dataset>¶

dataset_id = <ForeignKeyField: DatasetVersionCurrent.dataset>¶

description = <TextField: DatasetVersionCurrent.description>¶

file_access = <EnumField: DatasetVersionCurrent.file_access>¶

id = <AutoField: DatasetVersionCurrent.id>¶

num_variants = <IntegerField: DatasetVersionCurrent.num_variants>¶

portal_avail = <BooleanField: DatasetVersionCurrent.portal_avail>¶

ref_doi = <CharField: DatasetVersionCurrent.ref_doi>¶

reference_set = <ForeignKeyField: DatasetVersionCurrent.reference_set>¶

reference_set_id = <ForeignKeyField: DatasetVersionCurrent.reference_set>¶

terms = <TextField: DatasetVersionCurrent.terms>¶

version = <CharField: DatasetVersionCurrent.version>¶

class EnumField(choices=None, *args, **kwargs)[source]¶

Bases: peewee.Field

db_field = 'string'¶

db_value(value)[source]¶

python_value(value)[source]¶

class Feature(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of FeatureDoesNotExist

chrom = <CharField: Feature.chrom>¶

feature_type = <CharField: Feature.feature_type>¶

gene = <ForeignKeyField: Feature.gene>¶

gene_id = <ForeignKeyField: Feature.gene>¶

id = <AutoField: Feature.id>¶

start = <IntegerField: Feature.start>¶

stop = <IntegerField: Feature.stop>¶

strand = <EnumField: Feature.strand>¶

transcript = <ForeignKeyField: Feature.transcript>¶

transcript_id = <ForeignKeyField: Feature.transcript>¶

class Gene(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of GeneDoesNotExist

canonical_transcript = <CharField: Gene.canonical_transcript>¶

chrom = <CharField: Gene.chrom>¶

exons¶

full_name = <CharField: Gene.full_name>¶

gene_id = <CharField: Gene.gene_id>¶

id = <AutoField: Gene.id>¶

name = <CharField: Gene.name>¶

other_names¶

reference_set = <ForeignKeyField: Gene.reference_set>¶

reference_set_id = <ForeignKeyField: Gene.reference_set>¶

start = <IntegerField: Gene.start>¶

stop = <IntegerField: Gene.stop>¶

strand = <EnumField: Gene.strand>¶

transcripts¶

variants¶

class GeneOtherNames(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of GeneOtherNamesDoesNotExist

gene = <ForeignKeyField: GeneOtherNames.gene>¶

gene_id = <ForeignKeyField: GeneOtherNames.gene>¶

id = <AutoField: GeneOtherNames.id>¶

name = <CharField: GeneOtherNames.name>¶

class Linkhash(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of LinkhashDoesNotExist

dataset_version = <ForeignKeyField: Linkhash.dataset_version>¶

dataset_version_id = <ForeignKeyField: Linkhash.dataset_version>¶

expires_on = <DateTimeField: Linkhash.expires_on>¶

hash = <CharField: Linkhash.hash>¶

id = <AutoField: Linkhash.id>¶

user = <ForeignKeyField: Linkhash.user>¶

user_id = <ForeignKeyField: Linkhash.user>¶

class Metrics(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of MetricsDoesNotExist

dataset_version = <ForeignKeyField: Metrics.dataset_version>¶

dataset_version_id = <ForeignKeyField: Metrics.dataset_version>¶

hist = <ArrayField: Metrics.hist>¶

id = <AutoField: Metrics.id>¶

metric = <CharField: Metrics.metric>¶

mids = <ArrayField: Metrics.mids>¶

class ReferenceSet(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

The gencode, ensembl, dbNSFP and omim data are combined to fill out the Gene, Transcript and Feature tables. DbSNP data is separate, and may be shared between reference sets, so it uses a foreign key instead.

DoesNotExist¶: alias of ReferenceSetDoesNotExist

current_version¶

dataset_versions¶

dbnsfp_version = <CharField: ReferenceSet.dbnsfp_version>¶

ensembl_version = <CharField: ReferenceSet.ensembl_version>¶

gencode_version = <CharField: ReferenceSet.gencode_version>¶

genes¶

id = <AutoField: ReferenceSet.id>¶

name = <CharField: ReferenceSet.name>¶

reference_build = <CharField: ReferenceSet.reference_build>¶

class SFTPUser(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of SFTPUserDoesNotExist

account_expires = <DateTimeField: SFTPUser.account_expires>¶

id = <AutoField: SFTPUser.id>¶

password_hash = <CharField: SFTPUser.password_hash>¶

user = <ForeignKeyField: SFTPUser.user>¶

user_id = <ForeignKeyField: SFTPUser.user>¶

user_name = <CharField: SFTPUser.user_name>¶

user_uid = <IntegerField: SFTPUser.user_uid>¶

class SampleSet(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of SampleSetDoesNotExist

collection = <ForeignKeyField: SampleSet.collection>¶

collection_id = <ForeignKeyField: SampleSet.collection>¶

dataset = <ForeignKeyField: SampleSet.dataset>¶

dataset_id = <ForeignKeyField: SampleSet.dataset>¶

id = <AutoField: SampleSet.id>¶

phenotype = <CharField: SampleSet.phenotype>¶

sample_size = <IntegerField: SampleSet.sample_size>¶

class Study(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

A study is a scientific study with a PI and a description, and may include one or more datasets.

DoesNotExist¶: alias of StudyDoesNotExist

contact_email = <CharField: Study.contact_email>¶

contact_name = <CharField: Study.contact_name>¶

datasets¶

description = <TextField: Study.description>¶

id = <AutoField: Study.id>¶

pi_email = <CharField: Study.pi_email>¶

pi_name = <CharField: Study.pi_name>¶

publication_date = <DateTimeField: Study.publication_date>¶

ref_doi = <CharField: Study.ref_doi>¶

title = <CharField: Study.title>¶

class Transcript(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of TranscriptDoesNotExist

chrom = <CharField: Transcript.chrom>¶

gene = <ForeignKeyField: Transcript.gene>¶

gene_id = <ForeignKeyField: Transcript.gene>¶

id = <AutoField: Transcript.id>¶

mim_annotation = <CharField: Transcript.mim_annotation>¶

mim_gene_accession = <IntegerField: Transcript.mim_gene_accession>¶

start = <IntegerField: Transcript.start>¶

stop = <IntegerField: Transcript.stop>¶

strand = <EnumField: Transcript.strand>¶

transcript_id = <CharField: Transcript.transcript_id>¶

transcripts¶

variants¶

class User(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of UserDoesNotExist

access_current¶

access_logs¶

access_pending¶

affiliation = <CharField: User.affiliation>¶

consent_logs¶

country = <CharField: User.country>¶

dataset_access¶

download_logs¶

email = <CharField: User.email>¶

has_access(dataset, ds_version=None)[source]¶

Check whether user has permission to access a dataset

Parameters:	dataset (Database) – peewee Database object ds_version (str) – the dataset version
Returns:	allowed to access
Return type:	bool

has_requested_access(dataset)[source]¶

id = <AutoField: User.id>¶

identity = <CharField: User.identity>¶

identity_type = <EnumField: User.identity_type>¶

is_admin(dataset)[source]¶

link_hashes¶

name = <CharField: User.name>¶

sftp_user¶

class UserAccessLog(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of UserAccessLogDoesNotExist

action = <EnumField: UserAccessLog.action>¶

dataset = <ForeignKeyField: UserAccessLog.dataset>¶

dataset_id = <ForeignKeyField: UserAccessLog.dataset>¶

id = <AutoField: UserAccessLog.id>¶

ts = <DateTimeField: UserAccessLog.ts>¶

user = <ForeignKeyField: UserAccessLog.user>¶

user_id = <ForeignKeyField: UserAccessLog.user>¶

class UserConsentLog(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of UserConsentLogDoesNotExist

dataset_version = <ForeignKeyField: UserConsentLog.dataset_version>¶

dataset_version_id = <ForeignKeyField: UserConsentLog.dataset_version>¶

id = <AutoField: UserConsentLog.id>¶

ts = <DateTimeField: UserConsentLog.ts>¶

user = <ForeignKeyField: UserConsentLog.user>¶

user_id = <ForeignKeyField: UserConsentLog.user>¶

class UserDownloadLog(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of UserDownloadLogDoesNotExist

dataset_file = <ForeignKeyField: UserDownloadLog.dataset_file>¶

dataset_file_id = <ForeignKeyField: UserDownloadLog.dataset_file>¶

id = <AutoField: UserDownloadLog.id>¶

ts = <DateTimeField: UserDownloadLog.ts>¶

user = <ForeignKeyField: UserDownloadLog.user>¶

user_id = <ForeignKeyField: UserDownloadLog.user>¶

class Variant(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of VariantDoesNotExist

allele_count = <IntegerField: Variant.allele_count>¶

allele_freq = <FloatField: Variant.allele_freq>¶

allele_num = <IntegerField: Variant.allele_num>¶

alt = <CharField: Variant.alt>¶

chrom = <CharField: Variant.chrom>¶

dataset_version = <ForeignKeyField: Variant.dataset_version>¶

dataset_version_id = <ForeignKeyField: Variant.dataset_version>¶

filter_string = <CharField: Variant.filter_string>¶

genes¶

hom_count = <IntegerField: Variant.hom_count>¶

id = <AutoField: Variant.id>¶

orig_alt_alleles = <ArrayField: Variant.orig_alt_alleles>¶

pos = <IntegerField: Variant.pos>¶

quality_metrics = <BinaryJSONField: Variant.quality_metrics>¶

ref = <CharField: Variant.ref>¶

rsid = <IntegerField: Variant.rsid>¶

site_quality = <FloatField: Variant.site_quality>¶

transcripts¶

variant_id = <CharField: Variant.variant_id>¶

vep_annotations = <BinaryJSONField: Variant.vep_annotations>¶

class VariantGenes(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of VariantGenesDoesNotExist

gene = <ForeignKeyField: VariantGenes.gene>¶

gene_id = <ForeignKeyField: VariantGenes.gene>¶

id = <AutoField: VariantGenes.id>¶

variant = <ForeignKeyField: VariantGenes.variant>¶

variant_id = <ForeignKeyField: VariantGenes.variant>¶

class VariantMate(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of VariantMateDoesNotExist

allele_count = <IntegerField: VariantMate.allele_count>¶

allele_freq = <FloatField: VariantMate.allele_freq>¶

allele_num = <IntegerField: VariantMate.allele_num>¶

alt = <CharField: VariantMate.alt>¶

chrom = <CharField: VariantMate.chrom>¶

chrom_id = <CharField: VariantMate.chrom_id>¶

dataset_version = <ForeignKeyField: VariantMate.dataset_version>¶

dataset_version_id = <ForeignKeyField: VariantMate.dataset_version>¶

id = <AutoField: VariantMate.id>¶

mate_chrom = <CharField: VariantMate.mate_chrom>¶

mate_id = <CharField: VariantMate.mate_id>¶

mate_start = <IntegerField: VariantMate.mate_start>¶

pos = <IntegerField: VariantMate.pos>¶

ref = <CharField: VariantMate.ref>¶

variant_id = <CharField: VariantMate.variant_id>¶

class VariantTranscripts(*args, **kwargs)[source]¶

Bases: backend.db.BaseModel

DoesNotExist¶: alias of VariantTranscriptsDoesNotExist

id = <AutoField: VariantTranscripts.id>¶

transcript = <ForeignKeyField: VariantTranscripts.transcript>¶

transcript_id = <ForeignKeyField: VariantTranscripts.transcript>¶

variant = <ForeignKeyField: VariantTranscripts.variant>¶

variant_id = <ForeignKeyField: VariantTranscripts.variant>¶

build_dict_from_row(row)[source]¶

get_admin_datasets(user)[source]¶

Get a list of datasets where user is admin

Parameters:	user (User) – Peewee User object for the user of interest
Returns:
Return type:	DataSetAccess

get_dataset(dataset: str)[source]¶

Given dataset name get Dataset

Parameters:	dataset (str) – short name of the dataset
Returns:	the corresponding DatasetVersion entry
Return type:	Dataset

get_dataset_version(dataset: str, version: str = None)[source]¶

Given dataset get DatasetVersion

Parameters:	dataset (str) – short name of the dataset
Returns:	the corresponding DatasetVersion entry
Return type:	DatasetVersion

get_next_free_uid()[source]¶

Get the next free uid >= 10000 and > than the current uids from the sftp_user table in the db.

Returns:	the next free uid
Return type:	int