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

Can now calculate turnaround time including holidays.

Browse Source
This commit is contained in:
lwark
2024-11-25 13:34:02 -06:00
parent 7d1e6dc606
commit 7f0b7feb5d
13 changed files with 533 additions and 300 deletions
Download Patch File Download Diff File Expand all files Collapse all files

102
src/submissions/backend/db/models/submissions.py
View File

@@ -2,30 +2,30 @@
Models for the main submission and sample types.
"""
from __future__ import annotations
import sys
import types
import zipfile
# import sys
# import types
# import zipfile
from copy import deepcopy
from getpass import getuser
import logging, uuid, tempfile, re, base64
import logging, uuid, tempfile, re, base64, numpy as np, pandas as pd, types, sys
from zipfile import ZipFile
from tempfile import TemporaryDirectory, TemporaryFile
from operator import itemgetter
from pprint import pformat
from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, event, inspect
from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, event, inspect, func
from sqlalchemy.orm import relationship, validates, Query
from sqlalchemy.orm.attributes import flag_modified
from sqlalchemy.ext.associationproxy import association_proxy
from sqlalchemy.exc import OperationalError as AlcOperationalError, IntegrityError as AlcIntegrityError, StatementError, \
ArgumentError
from sqlite3 import OperationalError as SQLOperationalError, IntegrityError as SQLIntegrityError
import pandas as pd
# import pandas as pd
from openpyxl import Workbook
from openpyxl.drawing.image import Image as OpenpyxlImage
from tools import row_map, setup_lookup, jinja_template_loading, rreplace, row_keys, check_key_or_attr, Result, Report, \
report_result
from datetime import datetime, date
report_result, create_holidays_for_year
from datetime import datetime, date, timedelta
from typing import List, Any, Tuple, Literal, Generator
from dateutil.parser import parse
from pathlib import Path
@@ -73,6 +73,7 @@ class BasicSubmission(BaseClass, LogMixin):
custom = Column(JSON)
controls = relationship("Control", back_populates="submission",
uselist=True) #: A control sample added to submission
completed_date = Column(TIMESTAMP)
submission_sample_associations = relationship(
"SubmissionSampleAssociation",
@@ -345,6 +346,8 @@ class BasicSubmission(BaseClass, LogMixin):
tips = self.generate_associations(name="submission_tips_associations")
cost_centre = self.cost_centre
custom = self.custom
controls = [item.to_sub_dict() for item in self.controls]
else:
reagents = None
samples = None
@@ -352,6 +355,7 @@ class BasicSubmission(BaseClass, LogMixin):
tips = None
cost_centre = None
custom = None
controls = None
# logger.debug("Getting comments")
try:
comments = self.comment
@@ -381,6 +385,8 @@ class BasicSubmission(BaseClass, LogMixin):
output["contact"] = contact
output["contact_phone"] = contact_phone
output["custom"] = custom
output["controls"] = controls
output["completed_date"] = self.completed_date
return output
def calculate_column_count(self) -> int:
@@ -619,7 +625,7 @@ class BasicSubmission(BaseClass, LogMixin):
Returns:
PydSubmission: converted object.
"""
from backend.validators import PydSubmission, PydSample, PydReagent, PydEquipment
from backend.validators import PydSubmission
dicto = self.to_dict(full_data=True, backup=backup)
# logger.debug("To dict complete")
new_dict = {}
@@ -628,24 +634,43 @@ class BasicSubmission(BaseClass, LogMixin):
missing = value in ['', 'None', None]
match key:
case "reagents":
new_dict[key] = [PydReagent(**reagent) for reagent in value]
# new_dict[key] = [PydReagent(**reagent) for reagent in value]
field_value = [item.to_pydantic(extraction_kit=self.extraction_kit) for item in self.submission_reagent_associations]
case "samples":
new_dict[key] = [PydSample(**{k.lower().replace(" ", "_"): v for k, v in sample.items()}) for sample
in dicto['samples']]
field_value = [item.to_pydantic() for item in self.submission_sample_associations]
case "equipment":
field_value = [item.to_pydantic() for item in self.submission_equipment_associations]
case "controls":
try:
new_dict[key] = [PydEquipment(**equipment) for equipment in dicto['equipment']]
field_value = [item.to_pydantic() for item in self.__getattribute__(key)]
except TypeError as e:
logger.error(f"Possible no equipment error: {e}")
logger.error(f"Error converting {key} to pydantic :{e}")
continue
case "tips":
field_value = [item.to_pydantic() for item in self.submission_tips_associations]
case "submission_type" | "contact":
field_value = dict(value=self.__getattribute__(key).name, missing=missing)
case "plate_number":
new_dict['rsl_plate_num'] = dict(value=value, missing=missing)
key = 'rsl_plate_num'
field_value = dict(value=self.rsl_plate_num, missing=missing)
# continue
case "submitter_plate_number":
new_dict['submitter_plate_num'] = dict(value=value, missing=missing)
# new_dict['submitter_plate_num'] = dict(value=self.submitter_plate_num, missing=missing)
# continue
key = "submitter_plate_num"
field_value = dict(value=self.submitter_plate_num, missing=missing)
case "id":
pass
continue
case _:
logger.debug(f"Setting dict {key} to {value}")
new_dict[key.lower().replace(" ", "_")] = dict(value=value, missing=missing)
try:
key = key.lower().replace(" ", "_")
field_value = dict(value=self.__getattribute__(key), missing=missing)
# new_dict[key.lower().replace(" ", "_")] = dict(value=self.__getattribute__(key), missing=missing)
except AttributeError:
logger.error(f"{key} is not available in {self}")
continue
logger.debug(f"Setting dict {key}")
new_dict[key] = field_value
# logger.debug(f"{key} complete after {time()-start}")
new_dict['filepath'] = Path(tempfile.TemporaryFile().name)
# logger.debug("Done converting fields.")
@@ -1021,6 +1046,7 @@ class BasicSubmission(BaseClass, LogMixin):
Tuple(dict, Template): (Updated dictionary, Template to be rendered)
"""
base_dict['excluded'] = cls.get_default_info('details_ignore')
base_dict['excluded'] += ['controls']
env = jinja_template_loading()
temp_name = f"{cls.__name__.lower()}_details.html"
# logger.debug(f"Returning template: {temp_name}")
@@ -1081,11 +1107,11 @@ class BasicSubmission(BaseClass, LogMixin):
end_date = date.today()
if end_date is not None and start_date is None:
logger.warning(f"End date with no start date, using Jan 1, 2023")
start_date = date(2023, 1, 1)
start_date = cls.__database_session__.query(cls, func.min(cls.submitted_date)).first()[1]
if start_date is not None:
# logger.debug(f"Querying with start date: {start_date} and end date: {end_date}")
match start_date:
case date():
case date() | datetime():
# logger.debug(f"Lookup BasicSubmission by start_date({start_date})")
start_date = start_date.strftime("%Y-%m-%d")
case int():
@@ -1098,14 +1124,18 @@ class BasicSubmission(BaseClass, LogMixin):
match end_date:
case date() | datetime():
# logger.debug(f"Lookup BasicSubmission by end_date({end_date})")
end_date = end_date + timedelta(days=1)
end_date = end_date.strftime("%Y-%m-%d")
case int():
# logger.debug(f"Lookup BasicSubmission by ordinal end_date {end_date}")
end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date().strftime(
end_date = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + end_date - 2).date() + timedelta(
days=1)
end_date = end_date.strftime(
"%Y-%m-%d")
case _:
# logger.debug(f"Lookup BasicSubmission by parsed str end_date {end_date}")
end_date = parse(end_date).strftime("%Y-%m-%d")
end_date = parse(end_date) + timedelta(days=1)
end_date = end_date.strftime("%Y-%m-%d")
# logger.debug(f"Compensating for same date by using time")
if start_date == end_date:
start_date = datetime.strptime(start_date, "%Y-%m-%d").strftime("%Y-%m-%d %H:%M:%S.%f")
@@ -1339,10 +1369,22 @@ class BasicSubmission(BaseClass, LogMixin):
writer = pyd.to_writer()
writer.xl.save(filename=fname.with_suffix(".xlsx"))
def get_turnaround_time(self):
completed = self.completed_date or datetime.now()
return self.calculate_turnaround(start_date=self.submitted_date.date(), end_date=completed.date())
@classmethod
def calculate_turnaround(cls, start_date:date|None=None, end_date:date|None=None) -> int|None:
try:
delta = np.busday_count(start_date, end_date, holidays=create_holidays_for_year(start_date.year))
except ValueError:
return None
return delta + 1
# Below are the custom submission types
class BacterialCulture(BasicSubmission, LogMixin):
class BacterialCulture(BasicSubmission):
"""
derivative submission type from BasicSubmission
"""
@@ -1429,7 +1471,7 @@ class BacterialCulture(BasicSubmission, LogMixin):
return input_dict
class Wastewater(BasicSubmission, LogMixin):
class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
"""
@@ -1868,7 +1910,7 @@ class WastewaterArtic(BasicSubmission):
pass
try:
input_dict['source_plate_number'] = int(input_dict['source_plate_number'])
except ValueError:
except (ValueError, KeyError):
input_dict['source_plate_number'] = 0
# NOTE: Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
# at the end, this has to be done here. No moving to sqlalchemy object :(
@@ -2276,6 +2318,10 @@ class BasicSample(BaseClass):
# logger.debug(f"Done converting {self} after {time()-start}")
return sample
def to_pydantic(self):
from backend.validators import PydSample
return PydSample(**self.to_sub_dict())
def set_attribute(self, name: str, value):
"""
Custom attribute setter (depreciated over built-in __setattr__)
@@ -2733,6 +2779,10 @@ class SubmissionSampleAssociation(BaseClass):
sample['submission_rank'] = self.submission_rank
return sample
def to_pydantic(self):
from backend.validators import PydSample
return PydSample(**self.to_sub_dict())
def to_hitpick(self) -> dict | None:
"""
Outputs a dictionary usable for html plate maps.