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documentation and converted to username based exclusion of adding new kits

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This commit is contained in:
Landon Wark
2023-01-30 12:07:38 -06:00
parent bbb65d3fe6
commit 1f832dccf2
16 changed files with 876 additions and 296 deletions
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6
src/submissions/backend/db/models/controls.py
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@@ -1,5 +1,5 @@
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, UniqueConstraint
from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey
from sqlalchemy.orm import relationship
class ControlType(Base):
@@ -32,6 +32,6 @@ class Control(Base):
matches = Column(JSON) #: unstructured hashes in matches.tsv for each organism
kraken = Column(JSON) #: unstructured output from kraken_report
# UniqueConstraint('name', name='uq_control_name')
submission_id = Column(INTEGER, ForeignKey("_submissions.id"))
submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id])
submission_id = Column(INTEGER, ForeignKey("_submissions.id")) #: parent submission id
submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id]) #: parent submission

84
src/submissions/backend/db/models/kits.py
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@@ -3,57 +3,88 @@ from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Int
from sqlalchemy.orm import relationship
# Table containing reagenttype-kittype relationships
reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata, Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")), Column("kits_id", INTEGER, ForeignKey("_kits.id")))
class KitType(Base):
"""
Base of kits used in submission processing
"""
__tablename__ = "_kits"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64), unique=True)
submissions = relationship("BasicSubmission", back_populates="extraction_kit")
used_for = Column(JSON)
cost_per_run = Column(FLOAT(2))
reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes)
reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id"))
name = Column(String(64), unique=True) #: name of kit
submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
used_for = Column(JSON) #: list of names of sample types this kit can process
cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit
reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
def __str__(self):
def __str__(self) -> str:
"""
a string representing this object
Returns:
str: a string representing this object's name
"""
return self.name
class ReagentType(Base):
"""
Base of reagent type abstract
"""
__tablename__ = "_reagent_types"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64))
kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id"))
kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id])
instances = relationship("Reagent", back_populates="type")
name = Column(String(64)) #: name of reagent type
kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id")) #: id of joined kit type
kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id]) #: kits this reagent is used in
instances = relationship("Reagent", back_populates="type") #: concrete instances of this reagent type
# instances_id = Column(INTEGER, ForeignKey("_reagents.id", ondelete='SET NULL'))
eol_ext = Column(Interval())
eol_ext = Column(Interval()) #: extension of life interval
def __str__(self):
def __str__(self) -> str:
"""
string representing this object
Returns:
str: string representing this object's name
"""
return self.name
class Reagent(Base):
"""
Concrete reagent instance
"""
__tablename__ = "_reagents"
id = Column(INTEGER, primary_key=True) #: primary key
type = relationship("ReagentType", back_populates="instances")
type_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', name="fk_reagent_type_id"))
name = Column(String(64))
lot = Column(String(64))
expiry = Column(TIMESTAMP)
submissions = relationship("BasicSubmission", back_populates="reagents", uselist=True)
type = relationship("ReagentType", back_populates="instances") #: joined parent reagent type
type_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', name="fk_reagent_type_id")) #: id of parent reagent type
name = Column(String(64)) #: reagent name
lot = Column(String(64)) #: lot number of reagent
expiry = Column(TIMESTAMP) #: expiry date - extended by eol_ext of parent programmatically
submissions = relationship("BasicSubmission", back_populates="reagents", uselist=True) #: submissions this reagent is used in
def __str__(self):
def __str__(self) -> str:
"""
string representing this object
Returns:
str: string representing this object's lot number
"""
return self.lot
def to_sub_dict(self):
def to_sub_dict(self) -> dict:
"""
dictionary containing values necessary for gui
Returns:
dict: gui friendly dictionary
"""
try:
type = self.type.name.replace("_", " ").title()
except AttributeError:
@@ -62,7 +93,4 @@ class Reagent(Base):
"type": type,
"lot": self.lot,
"expiry": self.expiry.strftime("%Y-%m-%d")
}
}

37
src/submissions/backend/db/models/organizations.py
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@@ -3,32 +3,43 @@ from sqlalchemy import Column, String, TIMESTAMP, JSON, Float, INTEGER, ForeignK
from sqlalchemy.orm import relationship, validates
# table containing organization/contact relationship
orgs_contacts = Table("_orgs_contacts", Base.metadata, Column("org_id", INTEGER, ForeignKey("_organizations.id")), Column("contact_id", INTEGER, ForeignKey("_contacts.id")))
class Organization(Base):
"""
Base of organization
"""
__tablename__ = "_organizations"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64))
submissions = relationship("BasicSubmission", back_populates="submitting_lab")
cost_centre = Column(String())
contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts)
contact_ids = Column(INTEGER, ForeignKey("_contacts.id", ondelete="SET NULL", name="fk_org_contact_id"))
name = Column(String(64)) #: organization name
submissions = relationship("BasicSubmission", back_populates="submitting_lab") #: submissions this organization has submitted
cost_centre = Column(String()) #: cost centre used by org for payment
contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts) #: contacts involved with this org
contact_ids = Column(INTEGER, ForeignKey("_contacts.id", ondelete="SET NULL", name="fk_org_contact_id")) #: contact ids of this organization
def __str__(self):
def __str__(self) -> str:
"""
String representing organization
Returns:
str: string representing organization name
"""
return self.name.replace("_", " ").title()
class Contact(Base):
"""
Base of Contace
"""
__tablename__ = "_contacts"
id = id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64))
email = Column(String(64))
phone = Column(String(32))
organization = relationship("Organization", back_populates="contacts", uselist=True)
# organization_id = Column(INTEGER, ForeignKey("_organizations.id"))
name = Column(String(64)) #: contact name
email = Column(String(64)) #: contact email
phone = Column(String(32)) #: contact phone number
organization = relationship("Organization", back_populates="contacts", uselist=True, secondary=orgs_contacts) #: relationship to joined organization
organization_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_contact_org_id")) #: joined organization ids

62
src/submissions/backend/db/models/samples.py
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@@ -1,18 +1,20 @@
from . import Base
from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, FLOAT, BOOLEAN
from sqlalchemy.orm import relationship, relationships
from sqlalchemy.orm import relationship
class WWSample(Base):
"""
Base wastewater sample
"""
__tablename__ = "_ww_samples"
id = Column(INTEGER, primary_key=True) #: primary key
ww_processing_num = Column(String(64))
ww_sample_full_id = Column(String(64), nullable=False)
rsl_number = Column(String(64))
rsl_plate = relationship("Wastewater", back_populates="samples")
rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_sample_id"))
rsl_number = Column(String(64)) #: rsl plate identification number
rsl_plate = relationship("Wastewater", back_populates="samples") #: relationship to parent plate
rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_submission_id"))
collection_date = Column(TIMESTAMP) #: Date submission received
testing_type = Column(String(64))
site_status = Column(String(64))
@@ -22,12 +24,24 @@ class WWSample(Base):
seq_submitted = Column(BOOLEAN())
ww_seq_run_id = Column(String(64))
sample_type = Column(String(8))
well_number = Column(String(8))
well_number = Column(String(8)) #: location on plate
def to_string(self):
def to_string(self) -> str:
"""
string representing sample object
Returns:
str: string representing location and sample id
"""
return f"{self.well_number}: {self.ww_sample_full_id}"
def to_sub_dict(self):
def to_sub_dict(self) -> dict:
"""
gui friendly dictionary
Returns:
dict: well location and id
"""
return {
"well": self.well_number,
"name": self.ww_sample_full_id,
@@ -35,21 +49,35 @@ class WWSample(Base):
class BCSample(Base):
"""
base of bacterial culture sample
"""
__tablename__ = "_bc_samples"
id = Column(INTEGER, primary_key=True) #: primary key
well_number = Column(String(8))
sample_id = Column(String(64), nullable=False)
organism = Column(String(64))
concentration = Column(String(16))
rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id"))
rsl_plate = relationship("BacterialCulture", back_populates="samples")
well_number = Column(String(8)) #: location on parent plate
sample_id = Column(String(64), nullable=False) #: identification from submitter
organism = Column(String(64)) #: bacterial specimen
concentration = Column(String(16)) #:
rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id")) #: id of parent plate
rsl_plate = relationship("BacterialCulture", back_populates="samples") #: relationship to parent plate
def to_string(self):
def to_string(self) -> str:
"""
string representing object
Returns:
str: string representing well location, sample id and organism
"""
return f"{self.well_number}: {self.sample_id} - {self.organism}"
def to_sub_dict(self):
def to_sub_dict(self) -> dict:
"""
gui friendly dictionary
Returns:
dict: well location and name (sample id, organism)
"""
return {
"well": self.well_number,
"name": f"{self.sample_id} - ({self.organism})",

50
src/submissions/backend/db/models/submissions.py
View File

@@ -3,26 +3,29 @@ from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table
from sqlalchemy.orm import relationship
from datetime import datetime as dt
# table containing reagents/submission relationships
reagents_submissions = Table("_reagents_submissions", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("submission_id", INTEGER, ForeignKey("_submissions.id")))
class BasicSubmission(Base):
"""
Base of basic submission which polymorphs into BacterialCulture and Wastewater
"""
__tablename__ = "_submissions"
id = Column(INTEGER, primary_key=True) #: primary key
rsl_plate_num = Column(String(32), unique=True) #: RSL name (e.g. RSL-22-0012)
submitter_plate_num = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
submitted_date = Column(TIMESTAMP) #: Date submission received
submitting_lab = relationship("Organization", back_populates="submissions") #: client
submitting_lab = relationship("Organization", back_populates="submissions") #: client org
submitting_lab_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_BS_sublab_id"))
sample_count = Column(INTEGER) #: Number of samples in the submission
extraction_kit = relationship("KitType", back_populates="submissions") #: The extraction kit used
extraction_kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", name="fk_BS_extkit_id"))
submission_type = Column(String(32))
technician = Column(String(64))
submission_type = Column(String(32)) #: submission type (should be string in D3 of excel sheet)
technician = Column(String(64)) #: initials of processing tech
# Move this into custom types?
reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions)
reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id"))
reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
__mapper_args__ = {
"polymorphic_identity": "basic_submission",
@@ -30,10 +33,23 @@ class BasicSubmission(Base):
"with_polymorphic": "*",
}
def to_string(self):
def to_string(self) -> str:
"""
string presenting basic submission
Returns:
str: string representing rsl plate number and submitter plate number
"""
return f"{self.rsl_plate_num} - {self.submitter_plate_num}"
def to_dict(self):
def to_dict(self) -> dict:
"""
dictionary used in submissions summary
Returns:
dict: dictionary used in submissions summary
"""
# get lab from nested organization object
try:
sub_lab = self.submitting_lab.name
except AttributeError:
@@ -42,6 +58,7 @@ class BasicSubmission(Base):
sub_lab = sub_lab.replace("_", " ").title()
except AttributeError:
pass
# get extraction kit name from nested kit object
try:
ext_kit = self.extraction_kit.name
except AttributeError:
@@ -60,7 +77,14 @@ class BasicSubmission(Base):
return output
def report_dict(self):
def report_dict(self) -> dict:
"""
dictionary used in creating reports
Returns:
dict: dictionary used in creating reports
"""
# get lab name from nested organization object
try:
sub_lab = self.submitting_lab.name
except AttributeError:
@@ -69,10 +93,12 @@ class BasicSubmission(Base):
sub_lab = sub_lab.replace("_", " ").title()
except AttributeError:
pass
# get extraction kit name from nested kittype object
try:
ext_kit = self.extraction_kit.name
except AttributeError:
ext_kit = None
# get extraction kit cost from nested kittype object
try:
cost = self.extraction_kit.cost_per_run
except AttributeError:
@@ -93,6 +119,9 @@ class BasicSubmission(Base):
# Below are the custom submission
class BacterialCulture(BasicSubmission):
"""
derivative submission type from BasicSubmission
"""
# control_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_BC_control_id"))
controls = relationship("Control", back_populates="submission", uselist=True) #: A control sample added to submission
samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
@@ -101,6 +130,9 @@ class BacterialCulture(BasicSubmission):
class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
"""
samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
# ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
__mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}