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Generic info fields input into 'custom'.

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This commit is contained in:
lwark
2024-09-24 15:23:51 -05:00
parent 7bc356e205
commit b0e9f9996d
13 changed files with 898 additions and 12 deletions
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3
src/submissions/backend/db/models/kits.py
View File

@@ -932,6 +932,9 @@ class SubmissionType(BaseClass):
new_process.submission_types.append(submission_type)
new_process.kit_types.append(new_kit)
new_process.equipment_roles.append(new_role)
if 'orgs' in import_dict.keys():
logger.info("Found Organizations to be imported.")
Organization.import_from_json(filepath=filepath)
return submission_type

43
src/submissions/backend/db/models/organizations.py
View File

@@ -2,12 +2,15 @@
All client organization related models.
'''
from __future__ import annotations
import json, yaml, logging
from pathlib import Path
from pprint import pformat
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
from typing import List
import logging
logger = logging.getLogger(f"submissions.{__name__}")
@@ -74,6 +77,42 @@ class Organization(BaseClass):
def save(self):
super().save()
@classmethod
@check_authorization
def import_from_json(cls, filepath: Path|str):
if isinstance(filepath, str):
filepath = Path(filepath)
if not filepath.exists():
logging.critical(f"Given file could not be found.")
return None
with open(filepath, "r") as f:
if filepath.suffix == ".json":
import_dict = json.load(fp=f)
elif filepath.suffix == ".yml":
import_dict = yaml.safe_load(stream=f)
else:
raise Exception(f"Filetype {filepath.suffix} not supported.")
data = import_dict['orgs']
logger.debug(pformat(import_dict))
for org in data:
organ = Organization.query(name=org['name'])
if organ is None:
organ = Organization(name=org['name'])
try:
organ.cost_centre = org['cost_centre']
except KeyError:
organ.cost_centre = "xxx"
for contact in org['contacts']:
cont = Contact.query(name=contact['name'])
if cont is None:
cont = Contact()
for k, v in contact.items():
cont.__setattr__(k, v)
organ.contacts.append(cont)
organ.save()
# logger.debug(pformat(organ.__dict__))
class Contact(BaseClass):
"""
@@ -119,7 +158,7 @@ class Contact(BaseClass):
match name:
case str():
# logger.debug(f"Looking up contact with name: {name}")
query = query.filter(cls.name == name)
query = query.filter(cls.name == name.title())
limit = 1
case _:
pass

52
src/submissions/backend/db/models/submissions.py
View File

@@ -72,6 +72,7 @@ class BasicSubmission(BaseClass):
contact = relationship("Contact", back_populates="submissions") #: client org
contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
name="fk_BS_contact_id")) #: client lab id from _organizations
custom = Column(JSON)
submission_sample_associations = relationship(
"SubmissionSampleAssociation",
@@ -563,7 +564,11 @@ class BasicSubmission(BaseClass):
existing += value
else:
if value is not None:
existing.append(value)
if key == "custom":
existing = value
else:
existing.append(value)
self.__setattr__(key, existing)
flag_modified(self, key)
return
@@ -741,6 +746,28 @@ class BasicSubmission(BaseClass):
dict: Updated sample dictionary
"""
logger.info(f"Calling {cls.__mapper_args__['polymorphic_identity']} info parser.")
# logger.debug(f"Input dict: {input_dict}")
# logger.debug(f"Custom fields: {custom_fields}")
input_dict['custom'] = {}
for k,v in custom_fields.items():
logger.debug(f"Attempting custom parse of {k}: {v}")
match v['type']:
case "exempt":
continue
case "cell":
ws = xl[v['read']['sheet']]
input_dict['custom'][k] = ws.cell(row=v['read']['row'], column=v['read']['column']).value
case "range":
ws = xl[v['sheet']]
input_dict['custom'][k] = []
if v['start_row'] != v['end_row']:
v['end_row'] = v['end_row'] + 1
if v['start_column'] != v['end_column']:
v['end_column'] = v['end_column'] + 1
for ii in range(v['start_row'], v['end_row']):
for jj in range(v['start_column'], v['end_column']+1):
input_dict['custom'][k].append(dict(value=ws.cell(row=ii, column=jj).value, row=ii, column=jj))
return input_dict
@classmethod
@@ -790,6 +817,29 @@ class BasicSubmission(BaseClass):
Workbook: Updated workbook
"""
logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} autofill")
logger.debug(f"Input dict: {info}")
logger.debug(f"Custom fields: {custom_fields}")
for k,v in custom_fields.items():
try:
assert v['type'] in ['exempt', 'range', 'cell']
except (AssertionError, KeyError):
continue
match v['type']:
case "exempt":
continue
case "cell":
v['write'].append(v['read'])
for cell in v['write']:
ws = input_excel[cell['sheet']]
ws.cell(row=cell['row'], column=cell['column'], value=info['custom'][k])
case "range":
ws = input_excel[v['sheet']]
if v['start_row'] != v['end_row']:
v['end_row'] = v['end_row'] + 1
if v['start_column'] != v['end_column']:
v['end_column'] = v['end_column'] + 1
for item in info['custom'][k]:
ws.cell(row=item['row'], column=item['column'], value=item['value'])
return input_excel
@classmethod

20
src/submissions/backend/excel/parser.py
View File

@@ -65,20 +65,28 @@ class SheetParser(object):
"""
parser = InfoParser(xl=self.xl, submission_type=self.submission_type, sub_object=self.sub_object)
info = parser.parse_info()
logger.debug(f"Checking old submission type: {self.submission_type.name} against new: {info['submission_type']['value']}")
if self.submission_type.name != info['submission_type']['value']:
if info['submission_type']['value'] not in [None, "None", "", " "]:
self.submission_type = SubmissionType.query(name=info['submission_type']['value'])
logger.debug(f"Updated self.submission_type to {self.submission_type}. Rerunning parse.")
self.parse_info()
return
self.info_map = parser.map
for k, v in info.items():
match k:
# NOTE: exclude samples.
case "sample":
continue
case "submission_type":
self.sub[k] = v
# NOTE: Rescue submission type using scraped values to be used in Sample, Reagents, etc.
if v not in [None, "None", "", " "]:
self.submission_type = SubmissionType.query(name=v)
logger.debug(f"Updated self.submission_type to {self.submission_type}")
# case "submission_type":
# self.sub[k] = v
# # NOTE: Rescue submission type using scraped values to be used in Sample, Reagents, etc.
# if v not in [None, "None", "", " "]:
# self.submission_type = SubmissionType.query(name=v)
# logger.debug(f"Updated self.submission_type to {self.submission_type}")
case _:
self.sub[k] = v
print(f"\n\n {self.sub} \n\n")
def parse_reagents(self, extraction_kit: str | None = None):

2
src/submissions/backend/excel/writer.py
View File

@@ -175,6 +175,8 @@ class InfoWriter(object):
"""
final_info = {}
for k, v in self.info:
if k == "custom":
continue
# NOTE: merge all comments to fit in single cell.
if k == "comment" and isinstance(v['value'], list):
json_join = [item['text'] for item in v['value'] if 'text' in item.keys()]

14
src/submissions/backend/validators/pydant.py
View File

@@ -734,11 +734,19 @@ class PydSubmission(BaseModel, extra='allow'):
# logger.debug(f"Here's our list of duplicate removed samples: {self.samples}")
for key, value in dicto.items():
if isinstance(value, dict):
value = value['value']
try:
value = value['value']
except KeyError:
if key == "custom":
pass
else:
continue
if value is None:
continue
# logger.debug(f"Setting {key} to {value}")
match key:
# case "custom":
# instance.custom = value
case "reagents":
if report.results[0].code == 1:
instance.submission_reagent_associations = []
@@ -782,9 +790,13 @@ class PydSubmission(BaseModel, extra='allow'):
ii = value.items()
except AttributeError:
ii = {}
logger.debug(f"ii is {ii}, value is {value}")
for k, v in ii:
logger.debug(f"k is {k}, v is {v}")
if isinstance(v, datetime):
value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
else:
value[k] = v
instance.set_attribute(key=key, value=value)
case _:
try: