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Tips parser complete.

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This commit is contained in:
lwark
2024-06-13 09:11:53 -05:00
parent 78c92cd31f
commit e0e3080af0
7 changed files with 311 additions and 66 deletions
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118
src/submissions/backend/db/models/kits.py
View File

@@ -8,13 +8,12 @@ from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date
import logging, re
from tools import check_authorization, setup_lookup, Report, Result
from typing import List, Literal
from typing import List, Literal, Any
from pandas import ExcelFile
from pathlib import Path
from . import Base, BaseClass, Organization
from io import BytesIO
logger = logging.getLogger(f'submissions.{__name__}')
# logger.debug("Table for ReagentType/Reagent relations")
@@ -79,14 +78,6 @@ tiproles_tips = Table(
extend_existing=True
)
submissions_tips = Table(
"_submissions_tips",
Base.metadata,
Column("submission_id", INTEGER, ForeignKey("_basicsubmissions.id")),
Column("tips_id", INTEGER, ForeignKey("_tips.id")),
extend_existing=True
)
process_tiprole = Table(
"_process_tiprole",
Base.metadata,
@@ -95,6 +86,15 @@ process_tiprole = Table(
extend_existing=True
)
equipment_tips = Table(
"_equipment_tips",
Base.metadata,
Column("equipment_id", INTEGER, ForeignKey("_equipment.id")),
Column("tips_id", INTEGER, ForeignKey("_tips.id")),
extend_existing=True
)
class KitType(BaseClass):
"""
Base of kits used in submission processing
@@ -133,7 +133,8 @@ class KitType(BaseClass):
"""
return f"<KitType({self.name})>"
def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> List[ReagentRole]:
def get_reagents(self, required: bool = False, submission_type: str | SubmissionType | None = None) -> List[
ReagentRole]:
"""
Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
@@ -143,7 +144,7 @@ class KitType(BaseClass):
Returns:
List[ReagentRole]: List of reagents linked to this kit.
"""
"""
match submission_type:
case SubmissionType():
# logger.debug(f"Getting reagents by SubmissionType {submission_type}")
@@ -609,6 +610,12 @@ class SubmissionType(BaseClass):
cascade="all, delete-orphan"
) #: triple association of KitTypes, ReagentTypes, SubmissionTypes
submissiontype_tiprole_associations = relationship(
"SubmissionTypeTipRoleAssociation",
back_populates="submission_type",
cascade="all, delete-orphan"
)
def __repr__(self) -> str:
"""
Returns:
@@ -656,7 +663,7 @@ class SubmissionType(BaseClass):
Returns:
dict: Map of locations
"""
"""
info = self.info_map
# logger.debug(f"Info map: {info}")
output = {}
@@ -674,7 +681,7 @@ class SubmissionType(BaseClass):
Returns:
dict: sample location map
"""
"""
return self.sample_map
def construct_equipment_map(self) -> dict:
@@ -693,6 +700,15 @@ class SubmissionType(BaseClass):
output[item.equipment_role.name] = emap
return output
def construct_tips_map(self):
output = {}
for item in self.submissiontype_tiprole_associations:
tmap = item.uses
if tmap is None:
tmap = {}
output[item.tip_role.name] = tmap
return output
def get_equipment(self, extraction_kit: str | KitType | None = None) -> List['PydEquipmentRole']:
"""
Returns PydEquipmentRole of all equipment associated with this SubmissionType
@@ -735,7 +751,7 @@ class SubmissionType(BaseClass):
Returns:
BasicSubmission: Submission class
"""
"""
from .submissions import BasicSubmission
return BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.name)
@@ -1071,6 +1087,8 @@ class Equipment(BaseClass):
secondary=equipmentroles_equipment) #: relation to EquipmentRoles
processes = relationship("Process", back_populates="equipment",
secondary=equipment_processes) #: relation to Processes
tips = relationship("Tips", back_populates="equipment",
secondary=equipment_tips) #: relation to Processes
equipment_submission_associations = relationship(
"SubmissionEquipmentAssociation",
back_populates="equipment",
@@ -1467,7 +1485,7 @@ class Process(BaseClass):
backref='process') #: relation to SubmissionEquipmentAssociation
kit_types = relationship("KitType", back_populates='processes',
secondary=kittypes_processes) #: relation to KitType
tip_roles = relationship("TipRoles", back_populates='processes',
tip_roles = relationship("TipRole", back_populates='processes',
secondary=process_tiprole) #: relation to KitType
def __repr__(self) -> str:
@@ -1502,19 +1520,25 @@ class Process(BaseClass):
class TipRole(BaseClass):
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: name of reagent type
instances = relationship("Tips", back_populates="role",
secondary=tiproles_tips) #: concrete instances of this reagent type
processes = relationship("Process", back_populates="tip_roles", secondary=process_tiprole)
tiprole_submissiontype_associations = relationship(
"SubmissionTypeTipRoleAssociation",
back_populates="tip_role",
cascade="all, delete-orphan"
) #: associated submission
submission_types = association_proxy("tiprole_submissiontype_associations", "submission_type")
def __repr__(self):
return f"<TipRole({self.name})>"
class Tips(BaseClass):
class Tips(BaseClass):
id = Column(INTEGER, primary_key=True) #: primary key
role = relationship("TipRole", back_populates="instances",
secondary=tiproles_tips) #: joined parent reagent type
@@ -1522,10 +1546,64 @@ class Tips(BaseClass):
name="fk_tip_role_id")) #: id of parent reagent type
name = Column(String(64)) #: tip common name
lot = Column(String(64)) #: lot number of tips
submissions = relationship("BasicSubmission", back_populates="tips",
secondary=submissions_tips) #: associated submission
equipment = relationship("Equipment", back_populates="tips",
secondary=equipment_tips) #: associated submission
tips_submission_associations = relationship(
"SubmissionTipsAssociation",
back_populates="tips",
cascade="all, delete-orphan"
) #: associated submission
submissions = association_proxy("tips_submission_associations", 'submission')
def __repr__(self):
return f"<Tips({self.name})>"
@classmethod
def query(cls, name: str | None = None, lot: str | None = None, limit: int = 0, **kwargs) -> Any | List[Any]:
query = cls.__database_session__.query(cls)
match name:
case str():
# logger.debug(f"Lookup Equipment by name str {name}")
query = query.filter(cls.name == name)
case _:
pass
match lot:
case str():
# logger.debug(f"Lookup Equipment by nickname str {nickname}")
query = query.filter(cls.lot == lot)
limit = 1
case _:
pass
return cls.execute_query(query=query, limit=limit)
class SubmissionTypeTipRoleAssociation(BaseClass):
"""
Abstract association between SubmissionType and TipRole
"""
tiprole_id = Column(INTEGER, ForeignKey("_tiprole.id"), primary_key=True) #: id of associated equipment
submissiontype_id = Column(INTEGER, ForeignKey("_submissiontype.id"),
primary_key=True) #: id of associated submission
uses = Column(JSON) #: locations of equipment on the submission type excel sheet.
static = Column(INTEGER,
default=1) #: if 1 this piece of equipment will always be used, otherwise it will need to be selected from list?
submission_type = relationship(SubmissionType,
back_populates="submissiontype_tiprole_associations") #: associated submission
tip_role = relationship(TipRole,
back_populates="tiprole_submissiontype_associations") #: associated equipment
class SubmissionTipsAssociation(BaseClass):
tip_id = Column(INTEGER, ForeignKey("_tips.id"), primary_key=True) #: id of associated equipment
submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True) #: id of associated submission
submission = relationship("BasicSubmission",
back_populates="submission_tips_associations") #: associated submission
tips = relationship(Tips,
back_populates="tips_submission_associations") #: associated equipment
role_name = Column(String(32)) #, ForeignKey("_tiprole.name"))
# role = relationship(TipRole)
def to_sub_dict(self):
return dict(role=self.role_name, name=self.tips.name, lot=self.tips.lot)

30
src/submissions/backend/db/models/submissions.py
View File

@@ -10,7 +10,7 @@ from zipfile import ZipFile
from tempfile import TemporaryDirectory
from operator import attrgetter, itemgetter
from pprint import pformat
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, Tips, TipRole, SubmissionTipsAssociation
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
@@ -96,6 +96,14 @@ class BasicSubmission(BaseClass):
equipment = association_proxy("submission_equipment_associations",
"equipment") #: Association proxy to SubmissionEquipmentAssociation.equipment
submission_tips_associations = relationship(
"SubmissionTipsAssociation",
back_populates="submission",
cascade="all, delete-orphan")
tips = association_proxy("submission_tips_associations",
"tips")
# NOTE: Allows for subclassing into ex. BacterialCulture, Wastewater, etc.
__mapper_args__ = {
"polymorphic_identity": "Basic Submission",
@@ -248,7 +256,6 @@ class BasicSubmission(BaseClass):
ext_info = self.extraction_info
except TypeError:
ext_info = None
output = {
"id": self.id,
"plate_number": self.rsl_plate_num,
@@ -282,16 +289,24 @@ class BasicSubmission(BaseClass):
# logger.debug("Running equipment")
try:
equipment = [item.to_sub_dict() for item in self.submission_equipment_associations]
if len(equipment) == 0:
if not equipment:
equipment = None
except Exception as e:
logger.error(f"Error setting equipment: {e}")
equipment = None
try:
tips = [item.to_sub_dict() for item in self.submission_tips_associations]
if not tips:
tips = None
except Exception as e:
logger.error(f"Error setting tips: {e}")
tips = None
cost_centre = self.cost_centre
else:
reagents = None
samples = None
equipment = None
tips = None
cost_centre = None
# logger.debug("Getting comments")
try:
@@ -315,6 +330,7 @@ class BasicSubmission(BaseClass):
output["extraction_info"] = ext_info
output["comment"] = comments
output["equipment"] = equipment
output["tips"] = tips
output["cost_centre"] = cost_centre
output["signed_by"] = self.signed_by
# logger.debug(f"Setting contact to: {contact} of type: {type(contact)}")
@@ -440,7 +456,7 @@ class BasicSubmission(BaseClass):
excluded = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact']
'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact', 'tips']
for item in excluded:
try:
df = df.drop(item, axis=1)
@@ -1110,6 +1126,12 @@ class BasicSubmission(BaseClass):
_, assoc = equip.toSQL(submission=self)
# logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}")
assoc.save()
if equip.tips:
logger.debug("We have tips in this equipment")
for tips in equip.tips:
tassoc = tips.to_sql(submission=self)
tassoc.save()
else:
pass