class BiospecimenDiagnosis(db.Model, Base):
"""
Represents association table between biospecimen table and
diagnosis table. Contains all biospecimen, diagnosis combiniations.
:param kf_id: Unique id given by the Kid's First DCC
:param created_at: Time of object creation
:param modified_at: Last time of object modification
"""
__tablename__ = 'biospecimen_diagnosis'
__prefix__ = 'BD'
__table_args__ = (db.UniqueConstraint('diagnosis_id', 'biospecimen_id'), )
diagnosis_id = db.Column(KfId(),
db.ForeignKey('diagnosis.kf_id'),
nullable=False)
biospecimen_id = db.Column(KfId(),
db.ForeignKey('biospecimen.kf_id'),
nullable=False)
external_id = db.Column(db.Text(), doc='external id used by contributor')
biospecimen = db.relationship(Biospecimen,
backref=db.backref(
'biospecimen_diagnoses',
cascade='all, delete-orphan'))
diagnosis = db.relationship(Diagnosis,
backref=db.backref(
'biospecimen_diagnoses',
cascade='all, delete-orphan'))
class ReadGroupGenomicFile(db.Model, Base):
"""
Represents association table between read_group table and
genomic_file table. Contains all read_group, genomic_file combiniations.
:param kf_id: Unique id given by the Kid's First DCC
:param created_at: Time of object creation
:param modified_at: Last time of object modification
"""
__tablename__ = 'read_group_genomic_file'
__prefix__ = 'RF'
__table_args__ = (db.UniqueConstraint(
'read_group_id',
'genomic_file_id',
), )
read_group_id = db.Column(KfId(),
db.ForeignKey('read_group.kf_id'),
nullable=False)
genomic_file_id = db.Column(KfId(),
db.ForeignKey('genomic_file.kf_id'),
nullable=False)
external_id = db.Column(db.Text(), doc='external id used by contributor')
class TaskGenomicFile(db.Model, Base):
"""
Represents association table between task table and
genomic_file table. Contains all task, genomic_file combiniations.
:param kf_id: Unique id given by the Kid's First DCC
:param created_at: Time of object creation
:param modified_at: Last time of object modification
:param is_input: Denotes whether the genomic file was an input to the
executed task. True = Input, False = Output
"""
__tablename__ = 'task_genomic_file'
__prefix__ = 'TG'
__table_args__ = (db.UniqueConstraint('genomic_file_id', 'task_id',
'is_input'), )
genomic_file_id = db.Column(KfId(),
db.ForeignKey('genomic_file.kf_id'),
nullable=False)
task_id = db.Column(KfId(), db.ForeignKey('task.kf_id'), nullable=False)
is_input = db.Column(db.Boolean(), nullable=False, default=True)
class FamilyRelationship(db.Model, Base):
"""
Represents a relationship between two family members.
The relationship table represents a directed graph. One or more
relationships may exist between any two participants.
(P1 -> P2 is different than P2 -> P1)
:param kf_id: Primary key given by the Kid's First DCC
:param created_at: Time of object creation
:param modified_at: Last time of object modification
:param external_id: Name given to family_relationship by contributor
:param participant1_id: Kids first id of the first Participant in the
relationship
:param participant2_id: Kids first id of the second Participant
in the relationship
:param relationship_type: Text describing the nature of the
relationship (i.e. father, mother, sister, brother)
:param _rel_name: an autogenerated parameter used to ensure that the
relationships are not duplicated and the graph is undirected
:param source_text_notes: Text notes from source describing the
relationship
"""
__tablename__ = 'family_relationship'
__prefix__ = 'FR'
__table_args__ = (db.UniqueConstraint(
'participant1_id', 'participant2_id',
'participant1_to_participant2_relation',
'participant2_to_participant1_relation'), )
external_id = db.Column(db.Text(), doc='external id used by contributor')
participant1_id = db.Column(
KfId(),
db.ForeignKey('participant.kf_id'),
nullable=False,
doc='kf_id of one participant in the relationship')
participant2_id = db.Column(
KfId(),
db.ForeignKey('participant.kf_id'),
nullable=False,
doc='kf_id of the other participant in the relationship')
participant1_to_participant2_relation = db.Column(db.Text(),
nullable=False)
participant2_to_participant1_relation = db.Column(db.Text())
source_text_notes = db.Column(db.Text(),
doc='Text notes from source describing '
'the relationship')
participant1 = db.relationship(
Participant,
primaryjoin=participant1_id == Participant.kf_id,
backref=db.backref('outgoing_family_relationships',
cascade='all, delete-orphan'))
participant2 = db.relationship(
Participant,
primaryjoin=participant2_id == Participant.kf_id,
backref=db.backref('incoming_family_relationships',
cascade='all, delete-orphan'))
@classmethod
def query_all_relationships(cls,
participant_kf_id=None,
model_filter_params=None):
"""
Find all family relationships for a participant
:param participant_kf_id: Kids First ID of the participant
:param model_filter_params: Filter parameters to the query
Given a participant's kf_id, return all of the biological
family relationships of the participant and the relationships
of the participant's family members.
If the participant does not have a family defined, then return
all of the immediate/direct family relationships of the participant.
"""
# Apply model property filter params
if model_filter_params is None:
model_filter_params = {}
q = FamilyRelationship.query.filter_by(**model_filter_params)
# Get family relationships and join with participants
q = q.join(
Participant,
or_(FamilyRelationship.participant1,
FamilyRelationship.participant2))
# Do this bc query.get() errors out if passed None
if participant_kf_id:
pt = Participant.query.get(participant_kf_id)
family_id = pt.family_id if pt else None
# Use family to get all family relationships in participants family
if family_id:
q = q.filter(Participant.family_id == family_id)
# No family provided, use just family relationships
# to get only immediate family relationships for participant
else:
q = q.filter(
or_(
FamilyRelationship.participant1_id ==
participant_kf_id, FamilyRelationship.participant2_id
== participant_kf_id))
# Don't want duplicates - return unique family relationships
q = q.group_by(FamilyRelationship.kf_id)
return q
def __repr__(self):
return '<{} is {} of {}>'.format(
self.participant1.kf_id,
self.participant1_to_participant2_relation,
self.participant2.kf_id)
