landon/Submissions-App
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Code cleanup and documentation

Browse Source
This commit is contained in:
Landon Wark
2024-02-09 14:03:35 -06:00
parent eda62fba5a
commit a534d229a8
30 changed files with 1558 additions and 1347 deletions
Download Patch File Download Diff File Expand all files Collapse all files

38
src/submissions/backend/db/models/__init__.py
View File

@@ -2,7 +2,7 @@
Contains all models for sqlalchemy
'''
import sys
from sqlalchemy.orm import DeclarativeMeta, declarative_base
from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query
from sqlalchemy.ext.declarative import declared_attr
if 'pytest' in sys.modules:
from pathlib import Path
@@ -23,10 +23,16 @@ class BaseClass(Base):
@declared_attr
def __tablename__(cls):
"""
Set tablename to lowercase class name
"""
return f"_{cls.__name__.lower()}"
@declared_attr
def __database_session__(cls):
"""
Pull db session from ctx
"""
if not 'pytest' in sys.modules:
from tools import ctx
else:
@@ -35,6 +41,9 @@ class BaseClass(Base):
@declared_attr
def __directory_path__(cls):
"""
Pull submission directory from ctx
"""
if not 'pytest' in sys.modules:
from tools import ctx
else:
@@ -43,14 +52,39 @@ class BaseClass(Base):
@declared_attr
def __backup_path__(cls):
"""
Pull backup directory from ctx
"""
if not 'pytest' in sys.modules:
from tools import ctx
else:
from test_settings import ctx
return ctx.backup_path
def query_return(query:Query, limit:int=0):
"""
Execute sqlalchemy query.
Args:
query (Query): Query object
limit (int, optional): Maximum number of results to return (0 = all). Defaults to 0.
Returns:
_type_: Query result.
"""
with query.session.no_autoflush:
match limit:
case 0:
return query.all()
case 1:
return query.first()
case _:
return query.limit(limit).all()
def save(self):
# logger.debug(f"Saving {self}")
"""
Add the object to the database and commit
"""
try:
self.__database_session__.add(self)
self.__database_session__.commit()

71
src/submissions/backend/db/models/controls.py
View File

@@ -7,7 +7,7 @@ from sqlalchemy.orm import relationship, Query
import logging, json
from operator import itemgetter
from . import BaseClass
from tools import setup_lookup, query_return
from tools import setup_lookup
from datetime import date, datetime
from typing import List
from dateutil.parser import parse
@@ -18,7 +18,6 @@ class ControlType(BaseClass):
"""
Base class of a control archetype.
"""
# __tablename__ = '_control_types'
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(255), unique=True) #: controltype name (e.g. MCS)
@@ -48,7 +47,7 @@ class ControlType(BaseClass):
limit = 1
case _:
pass
return query_return(query=query, limit=limit)
return cls.query_return(query=query, limit=limit)
def get_subtypes(self, mode:str) -> List[str]:
"""
@@ -60,10 +59,13 @@ class ControlType(BaseClass):
Returns:
List[str]: list of subtypes available
"""
# Get first instance since all should have same subtypes
outs = self.instances[0]
# Get mode of instance
jsoner = json.loads(getattr(outs, mode))
logger.debug(f"JSON out: {jsoner.keys()}")
try:
# Pick genera (all should have same subtypes)
genera = list(jsoner.keys())[0]
except IndexError:
return []
@@ -74,8 +76,6 @@ class Control(BaseClass):
"""
Base class of a control sample.
"""
# __tablename__ = '_control_samples'
id = Column(INTEGER, primary_key=True) #: primary key
parent_id = Column(String, ForeignKey("_controltype.id", name="fk_control_parent_id")) #: primary key of control type
@@ -90,10 +90,14 @@ class Control(BaseClass):
refseq_version = Column(String(16)) #: version of refseq used in fastq parsing
kraken2_version = Column(String(16)) #: version of kraken2 used in fastq parsing
kraken2_db_version = Column(String(32)) #: folder name of kraken2 db
sample = relationship("BacterialCultureSample", back_populates="control")
sample_id = Column(INTEGER, ForeignKey("_basicsample.id", ondelete="SET NULL", name="cont_BCS_id"))
sample = relationship("BacterialCultureSample", back_populates="control") #: This control's submission sample
sample_id = Column(INTEGER, ForeignKey("_basicsample.id", ondelete="SET NULL", name="cont_BCS_id")) #: sample id key
def __repr__(self) -> str:
"""
Returns:
str: Representation of self
"""
return f"<Control({self.name})>"
def to_sub_dict(self) -> dict:
@@ -103,25 +107,25 @@ class Control(BaseClass):
Returns:
dict: output dictionary containing: Name, Type, Targets, Top Kraken results
"""
# load json string into dict
# logger.debug("loading json string into dict")
try:
kraken = json.loads(self.kraken)
except TypeError:
kraken = {}
# calculate kraken count total to use in percentage
# logger.debug("calculating kraken count total to use in percentage")
kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
new_kraken = []
for item in kraken:
# calculate kraken percent (overwrites what's already been scraped)
# logger.debug("calculating kraken percent (overwrites what's already been scraped)")
kraken_percent = kraken[item]['kraken_count'] / kraken_cnt_total
new_kraken.append({'name': item, 'kraken_count':kraken[item]['kraken_count'], 'kraken_percent':"{0:.0%}".format(kraken_percent)})
new_kraken = sorted(new_kraken, key=itemgetter('kraken_count'), reverse=True)
# set targets
# logger.debug("setting targets")
if self.controltype.targets == []:
targets = ["None"]
else:
targets = self.controltype.targets
# construct output dictionary
# logger.debug("constructing output dictionary")
output = {
"name" : self.name,
"type" : self.controltype.name,
@@ -141,49 +145,28 @@ class Control(BaseClass):
list[dict]: list of records
"""
output = []
# load json string for mode (i.e. contains, matches, kraken2)
# logger.debug("load json string for mode (i.e. contains, matches, kraken2)")
try:
data = json.loads(getattr(self, mode))
except TypeError:
data = {}
logger.debug(f"Length of data: {len(data)}")
# dict keys are genera of bacteria, e.g. 'Streptococcus'
# logger.debug("dict keys are genera of bacteria, e.g. 'Streptococcus'")
for genus in data:
_dict = {}
_dict['name'] = self.name
_dict['submitted_date'] = self.submitted_date
_dict['genus'] = genus
# get Target or Off-target of genus
# logger.debug("get Target or Off-target of genus")
_dict['target'] = 'Target' if genus.strip("*") in self.controltype.targets else "Off-target"
# set 'contains_hashes', etc for genus,
# logger.debug("set 'contains_hashes', etc for genus")
for key in data[genus]:
_dict[key] = data[genus][key]
output.append(_dict)
# Have to triage kraken data to keep program from getting overwhelmed
# logger.debug("Have to triage kraken data to keep program from getting overwhelmed")
if "kraken" in mode:
output = sorted(output, key=lambda d: d[f"{mode}_count"], reverse=True)[:49]
return output
def create_dummy_data(self, mode:str) -> dict:
"""
Create non-zero length data to maintain entry of zero length 'contains' (depreciated)
Args:
mode (str): analysis type, 'contains', etc
Returns:
dict: dictionary of 'Nothing' genus
"""
match mode:
case "contains":
data = {"Nothing": {"contains_hashes":"0/400", "contains_ratio":0.0}}
case "matches":
data = {"Nothing": {"matches_hashes":"0/400", "matches_ratio":0.0}}
case "kraken":
data = {"Nothing": {"kraken_percent":0.0, "kraken_count":0}}
case _:
data = {}
return data
@classmethod
def get_modes(cls) -> List[str]:
@@ -194,6 +177,7 @@ class Control(BaseClass):
List[str]: List of control mode names.
"""
try:
# logger.debug("Creating a list of JSON columns in _controls table")
cols = [item.name for item in list(cls.__table__.columns) if isinstance(item.type, JSON)]
except AttributeError as e:
logger.error(f"Failed to get available modes from db: {e}")
@@ -243,25 +227,32 @@ class Control(BaseClass):
if start_date != None:
match start_date:
case date():
# logger.debug(f"Lookup control by start date({start_date})")
start_date = start_date.strftime("%Y-%m-%d")
case int():
# logger.debug(f"Lookup control by ordinal start date {start_date}")
start_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + start_date - 2).date().strftime("%Y-%m-%d")
case _:
# logger.debug(f"Lookup control with parsed start date {start_date}")
start_date = parse(start_date).strftime("%Y-%m-%d")
match end_date:
case date():
# logger.debug(f"Lookup control by end date({end_date})")
end_date = end_date.strftime("%Y-%m-%d")
case int():
# logger.debug(f"Lookup control by ordinal end date {end_date}")
end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime("%Y-%m-%d")
case _:
# logger.debug(f"Lookup control with parsed end date {end_date}")
end_date = parse(end_date).strftime("%Y-%m-%d")
# logger.debug(f"Looking up BasicSubmissions from start date: {start_date} and end date: {end_date}")
query = query.filter(cls.submitted_date.between(start_date, end_date))
match control_name:
case str():
# logger.debug(f"Lookup control by name {control_name}")
query = query.filter(cls.name.startswith(control_name))
limit = 1
case _:
pass
return query_return(query=query, limit=limit)
return cls.query_return(query=query, limit=limit)

544
src/submissions/backend/db/models/kits.py
View File

File diff suppressed because it is too large Load Diff

31
src/submissions/backend/db/models/organizations.py
View File

@@ -5,7 +5,7 @@ from __future__ import annotations
from sqlalchemy import Column, String, INTEGER, ForeignKey, Table
from sqlalchemy.orm import relationship, Query
from . import Base, BaseClass
from tools import check_authorization, setup_lookup, query_return, Settings
from tools import check_authorization, setup_lookup
from typing import List
import logging
@@ -25,8 +25,7 @@ class Organization(BaseClass):
"""
Base of organization
"""
# __tablename__ = "_organizations"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: organization name
submissions = relationship("BasicSubmission", back_populates="submitting_lab") #: submissions this organization has submitted
@@ -34,11 +33,12 @@ class Organization(BaseClass):
contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts) #: contacts involved with this org
def __repr__(self) -> str:
"""
Returns:
str: Representation of this Organization
"""
return f"<Organization({self.name})>"
def set_attribute(self, name:str, value):
setattr(self, name, value)
@classmethod
@setup_lookup
def query(cls,
@@ -63,24 +63,17 @@ class Organization(BaseClass):
limit = 1
case _:
pass
return query_return(query=query, limit=limit)
return cls.query_return(query=query, limit=limit)
@check_authorization
def save(self, ctx:Settings):
"""
Adds this instance to the database and commits
Args:
ctx (Settings): Settings object passed down from GUI. Necessary to check authorization
"""
def save(self):
super().save()
class Contact(BaseClass):
"""
Base of Contact
"""
# __tablename__ = "_contacts"
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64)) #: contact name
email = Column(String(64)) #: contact email
@@ -88,6 +81,10 @@ class Contact(BaseClass):
organization = relationship("Organization", back_populates="contacts", uselist=True, secondary=orgs_contacts) #: relationship to joined organization
def __repr__(self) -> str:
"""
Returns:
str: Representation of this Contact
"""
return f"<Contact({self.name})>"
@classmethod
@@ -133,5 +130,5 @@ class Contact(BaseClass):
limit = 1
case _:
pass
return query_return(query=query, limit=limit)
return cls.query_return(query=query, limit=limit)

994
src/submissions/backend/db/models/submissions.py
View File

File diff suppressed because it is too large Load Diff