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Context menu for runs working.

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This commit is contained in:
lwark
2025-05-22 10:00:25 -05:00
parent 75c665ea05
commit d850166e08
40 changed files with 2852 additions and 3329 deletions
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37
src/submissions/backend/validators/__init__.py
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@@ -5,7 +5,7 @@ import logging, re
import sys
from pathlib import Path
from openpyxl import load_workbook
from backend.db.models import BasicRun, SubmissionType
from backend.db.models import Run, SubmissionType
from tools import jinja_template_loading
from jinja2 import Template
from dateutil.parser import parse
@@ -25,22 +25,22 @@ class RSLNamer(object):
self.submission_type = submission_type
if not self.submission_type:
self.submission_type = self.retrieve_submission_type(filename=filename)
logger.info(f"got run type: {self.submission_type}")
logger.info(f"got procedure type: {self.submission_type}")
if self.submission_type:
self.sub_object = BasicRun.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(
submission_type=submission_type))
if not data:
data = dict(submission_type=self.submission_type)
if "submission_type" not in data.keys():
data['submission_type'] = self.submission_type
if "proceduretype" not in data.keys():
data['proceduretype'] = self.submission_type
self.parsed_name = self.sub_object.enforce_name(instr=self.parsed_name, data=data)
logger.info(f"Parsed name: {self.parsed_name}")
@classmethod
def retrieve_submission_type(cls, filename: str | Path) -> str:
"""
Gets run type from excel file properties or sheet names or regex pattern match or user input
Gets procedure type from excel file properties or sheet names or regex pattern match or user input
Args:
filename (str | Path): filename
@@ -49,7 +49,7 @@ class RSLNamer(object):
TypeError: Raised if unsupported variable type for filename given.
Returns:
str: parsed run type
str: parsed procedure type
"""
def st_from_path(filepath: Path) -> str:
@@ -89,7 +89,7 @@ class RSLNamer(object):
sub_type = m.lastgroup
except AttributeError as e:
sub_type = None
logger.critical(f"No run type found or run type found!: {e}")
logger.critical(f"No procedure type found or procedure type found!: {e}")
return sub_type
match filename:
@@ -107,8 +107,8 @@ class RSLNamer(object):
if "pytest" in sys.modules:
raise ValueError("Submission Type came back as None.")
from frontend.widgets import ObjectSelector
dlg = ObjectSelector(title="Couldn't parse run type.",
message="Please select run type from list below.",
dlg = ObjectSelector(title="Couldn't parse procedure type.",
message="Please select procedure type from list below.",
obj_type=SubmissionType)
if dlg.exec():
submission_type = dlg.parse_form()
@@ -118,7 +118,7 @@ class RSLNamer(object):
@classmethod
def retrieve_rsl_number(cls, filename: str | Path, regex: re.Pattern | None = None):
"""
Uses regex to retrieve the plate number and run type from an input string
Uses regex to retrieve the plate number and procedure type from an input string
Args:
regex (str): string to construct pattern
@@ -145,14 +145,15 @@ class RSLNamer(object):
@classmethod
def construct_new_plate_name(cls, data: dict) -> str:
"""
Make a brand-new plate name from run data.
Make a brand-new plate name from procedure data.
Args:
data (dict): incoming run data
data (dict): incoming procedure data
Returns:
str: Output filename
"""
logger.debug(data)
if "submitted_date" in data.keys():
if isinstance(data['submitted_date'], dict):
if data['submitted_date']['value'] is not None:
@@ -163,14 +164,16 @@ class RSLNamer(object):
today = data['submitted_date']
else:
try:
today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", data['rsl_plate_num'])
today = re.search(r"\d{4}(_|-)?\d{2}(_|-)?\d{2}", data['name'])
today = parse(today.group())
except (AttributeError, KeyError):
today = datetime.now()
if "rsl_plate_num" in data.keys():
plate_number = data['rsl_plate_num'].split("-")[-1][0]
if isinstance(today, str):
today = datetime.strptime(today, "%Y-%m-%d")
if "name" in data.keys():
plate_number = data['name'].split("-")[-1][0]
else:
previous = BasicRun.query(start_date=today, end_date=today, submissiontype=data['submission_type'])
previous = Run.query(start_date=today, end_date=today, submissiontype=data['submissiontype'])
plate_number = len(previous) + 1
return f"RSL-{data['abbreviation']}-{today.year}{str(today.month).zfill(2)}{str(today.day).zfill(2)}-{plate_number}"
@@ -205,4 +208,4 @@ class RSLNamer(object):
from .pydant import PydSubmission, PydKitType, PydContact, PydOrganization, PydSample, PydReagent, PydReagentRole, \
PydEquipment, PydEquipmentRole, PydTips, PydPCRControl, PydIridaControl, PydProcess, PydElastic, PydClientSubmission
PydEquipment, PydEquipmentRole, PydTips, PydProcess, PydElastic, PydClientSubmission