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Bug fixes.

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This commit is contained in:
lwark
2024-08-15 09:30:43 -05:00
parent 1a55b52f31
commit 6c0795e92e
7 changed files with 62 additions and 38 deletions
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18
src/submissions/backend/db/models/kits.py
View File

@@ -11,7 +11,7 @@ from sqlalchemy.ext.associationproxy import association_proxy
from datetime import date from datetime import date
import logging, re import logging, re
from tools import check_authorization, setup_lookup, Report, Result from tools import check_authorization, setup_lookup, Report, Result
from typing import List, Literal, Generator from typing import List, Literal, Generator, Any
from pandas import ExcelFile from pandas import ExcelFile
from pathlib import Path from pathlib import Path
from . import Base, BaseClass, Organization from . import Base, BaseClass, Organization
@@ -261,7 +261,7 @@ class KitType(BaseClass):
base_dict['reagent roles'] = [] base_dict['reagent roles'] = []
base_dict['equipment roles'] = [] base_dict['equipment roles'] = []
for k, v in self.construct_xl_map_for_use(submission_type=submission_type): for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
logger.debug(f"Value: {v}") # logger.debug(f"Value: {v}")
try: try:
assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0] assoc = [item for item in self.kit_reagentrole_associations if item.reagent_role.name == k][0]
except IndexError as e: except IndexError as e:
@@ -275,10 +275,10 @@ class KitType(BaseClass):
except IndexError: except IndexError:
continue continue
for kk, vv in assoc.to_export_dict(kit_type=self).items(): for kk, vv in assoc.to_export_dict(kit_type=self).items():
logger.debug(f"{kk}:{vv}") # logger.debug(f"{kk}:{vv}")
v[kk] = vv v[kk] = vv
base_dict['equipment roles'].append(v) base_dict['equipment roles'].append(v)
logger.debug(f"KT returning {base_dict}") # logger.debug(f"KT returning {base_dict}")
return base_dict return base_dict
@@ -1492,6 +1492,16 @@ class SubmissionEquipmentAssociation(BaseClass):
processes=[process], role=self.role, nickname=self.equipment.nickname) processes=[process], role=self.role, nickname=self.equipment.nickname)
return output return output
@classmethod
@setup_lookup
def query(cls, equipment_id:int, submission_id:int, role:str, limit:int=0, **kwargs) -> Any | List[Any]:
query: Query = cls.__database_session__.query(cls)
query = query.filter(cls.equipment_id==equipment_id)
query = query.filter(cls.submission_id==submission_id)
query = query.filter(cls.role==role)
return cls.execute_query(query=query, limit=limit, **kwargs)
class SubmissionTypeEquipmentRoleAssociation(BaseClass): class SubmissionTypeEquipmentRoleAssociation(BaseClass):
""" """

35
src/submissions/backend/db/models/submissions.py
View File

@@ -295,8 +295,10 @@ class BasicSubmission(BaseClass):
if k == 'info': if k == 'info':
continue continue
if not any([item['role'] == k for item in reagents]): if not any([item['role'] == k for item in reagents]):
# expiry = date(year=1970, month=1, day=1)
expiry = "NA"
reagents.append( reagents.append(
dict(role=k, name="Not Applicable", lot="NA", expiry=date(year=1970, month=1, day=1), dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
missing=True)) missing=True))
except Exception as e: except Exception as e:
logger.error(f"We got an error retrieving reagents: {e}") logger.error(f"We got an error retrieving reagents: {e}")
@@ -507,10 +509,10 @@ class BasicSubmission(BaseClass):
sample, _ = sample.to_sql(submission=self) sample, _ = sample.to_sql(submission=self)
return return
case "reagents": case "reagents":
logger.debug(f"Reagents coming into SQL: {value}") # logger.debug(f"Reagents coming into SQL: {value}")
field_value = [reagent['value'].to_sql()[0] if isinstance(reagent, dict) else reagent.to_sql()[0] for field_value = [reagent['value'].to_sql()[0] if isinstance(reagent, dict) else reagent.to_sql()[0] for
reagent in value] reagent in value]
logger.debug(f"Reagents coming out of SQL: {field_value}") # logger.debug(f"Reagents coming out of SQL: {field_value}")
case "submission_type": case "submission_type":
field_value = SubmissionType.query(name=value) field_value = SubmissionType.query(name=value)
case "sample_count": case "sample_count":
@@ -521,7 +523,7 @@ class BasicSubmission(BaseClass):
case "ctx" | "csv" | "filepath" | "equipment": case "ctx" | "csv" | "filepath" | "equipment":
return return
case item if item in self.jsons(): case item if item in self.jsons():
logger.debug(f"Setting JSON attribute.") # logger.debug(f"Setting JSON attribute.")
existing = self.__getattribute__(key) existing = self.__getattribute__(key)
if value is None or value in ['', 'null']: if value is None or value in ['', 'null']:
logger.error(f"No value given, not setting.") logger.error(f"No value given, not setting.")
@@ -617,7 +619,7 @@ class BasicSubmission(BaseClass):
Args: Args:
original (bool, optional): Is this the first save. Defaults to True. original (bool, optional): Is this the first save. Defaults to True.
""" """
logger.debug("Saving submission.") # logger.debug("Saving submission.")
if original: if original:
self.uploaded_by = getuser() self.uploaded_by = getuser()
super().save() super().save()
@@ -1177,9 +1179,12 @@ class BasicSubmission(BaseClass):
# logger.debug(f"Processing: {equip}") # logger.debug(f"Processing: {equip}")
_, assoc = equip.toSQL(submission=self) _, assoc = equip.toSQL(submission=self)
# logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}") # logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}")
try:
assoc.save() assoc.save()
except AttributeError as e:
logger.error(f"Couldn't save association with {equip} due to {e}")
if equip.tips: if equip.tips:
logger.debug("We have tips in this equipment") # logger.debug("We have tips in this equipment")
for tips in equip.tips: for tips in equip.tips:
tassoc = tips.to_sql(submission=self) tassoc = tips.to_sql(submission=self)
tassoc.save() tassoc.save()
@@ -1308,7 +1313,7 @@ class BacterialCulture(BasicSubmission):
idx = df[df[0] == sample.well] idx = df[df[0] == sample.well]
if idx.empty: if idx.empty:
new = f"{sample.well[0]}{sample.well[1:].zfill(2)}" new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
logger.debug(f"Checking: {new}") # logger.debug(f"Checking: {new}")
idx = df[df[0] == new] idx = df[df[0] == new]
# logger.debug(f"Here is the row: {idx}") # logger.debug(f"Here is the row: {idx}")
row = idx.index.to_list()[0] row = idx.index.to_list()[0]
@@ -1366,7 +1371,7 @@ class Wastewater(BasicSubmission):
dict: Updated sample dictionary dict: Updated sample dictionary
""" """
input_dict = super().custom_info_parser(input_dict) input_dict = super().custom_info_parser(input_dict)
logger.debug(f"Input dict: {pformat(input_dict)}") # logger.debug(f"Input dict: {pformat(input_dict)}")
if xl is not None: if xl is not None:
try: try:
input_dict['csv'] = xl["Copy to import file"] input_dict['csv'] = xl["Copy to import file"]
@@ -1636,12 +1641,14 @@ class WastewaterArtic(BasicSubmission):
input_dict = super().custom_info_parser(input_dict) input_dict = super().custom_info_parser(input_dict)
egel_section = custom_fields['egel_results'] egel_section = custom_fields['egel_results']
ws = xl[egel_section['sheet']] ws = xl[egel_section['sheet']]
data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']) for data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']+1) for
ii in range(egel_section['start_row'], egel_section['end_row'])] ii in range(egel_section['start_row'], egel_section['end_row']+1)]
data = [cell for cell in data if cell.value is not None and "NTC" in cell.value] data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
# logger.debug(f"Got gel control map: {data}")
input_dict['gel_controls'] = [ input_dict['gel_controls'] = [
dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in
data] data]
# logger.debug(f"Got gel control info: {input_dict['gel_controls']}")
# NOTE: Get source plate information # NOTE: Get source plate information
source_plates_section = custom_fields['source_plates'] source_plates_section = custom_fields['source_plates']
ws = xl[source_plates_section['sheet']] ws = xl[source_plates_section['sheet']]
@@ -1854,10 +1861,10 @@ class WastewaterArtic(BasicSubmission):
""" """
input_excel = super().custom_info_writer(input_excel, info, backup) input_excel = super().custom_info_writer(input_excel, info, backup)
if isinstance(info, types.GeneratorType): if isinstance(info, types.GeneratorType):
logger.debug(f"Unpacking info generator.") # logger.debug(f"Unpacking info generator.")
info = {k: v for k, v in info} info = {k: v for k, v in info}
logger.debug(f"Info:\n{pformat(info)}") # logger.debug(f"Info:\n{pformat(info)}")
logger.debug(f"Custom fields:\n{pformat(custom_fields)}") # logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
# NOTE: check for source plate information # NOTE: check for source plate information
if check_key_or_attr(key='source_plates', interest=info, check_none=True): if check_key_or_attr(key='source_plates', interest=info, check_none=True):
source_plates_section = custom_fields['source_plates'] source_plates_section = custom_fields['source_plates']
@@ -2016,7 +2023,7 @@ class WastewaterArtic(BasicSubmission):
img = zipped.read(input_dict['gel_image_path']) img = zipped.read(input_dict['gel_image_path'])
with tempfile.TemporaryFile(mode="wb", suffix=".jpg", delete=False) as tmp: with tempfile.TemporaryFile(mode="wb", suffix=".jpg", delete=False) as tmp:
tmp.write(img) tmp.write(img)
logger.debug(f"Tempfile: {tmp.name}") # logger.debug(f"Tempfile: {tmp.name}")
img = InlineImage(tpl_obj, image_descriptor=tmp.name, width=Inches(5.5)) #, width=5.5)#, height=400) img = InlineImage(tpl_obj, image_descriptor=tmp.name, width=Inches(5.5)) #, width=5.5)#, height=400)
input_dict['gel_image'] = img input_dict['gel_image'] = img
return input_dict return input_dict

18
src/submissions/backend/excel/parser.py
View File

@@ -209,7 +209,7 @@ class InfoParser(object):
""" """
dicto = {} dicto = {}
# NOTE: This loop parses generic info # NOTE: This loop parses generic info
logger.debug(f"Map: {self.map}") # logger.debug(f"Map: {self.map}")
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
ws = self.xl[sheet] ws = self.xl[sheet]
relevant = [] relevant = []
@@ -590,7 +590,7 @@ class EquipmentParser(object):
Returns: Returns:
List[dict]: list of equipment List[dict]: list of equipment
""" """
logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}") # logger.debug(f"Equipment parser going into parsing: {pformat(self.__dict__)}")
output = [] output = []
# logger.debug(f"Sheets: {sheets}") # logger.debug(f"Sheets: {sheets}")
for sheet in self.xl.sheetnames: for sheet in self.xl.sheetnames:
@@ -600,17 +600,17 @@ class EquipmentParser(object):
except (TypeError, KeyError) as e: except (TypeError, KeyError) as e:
logger.error(f"Error creating relevant equipment list: {e}") logger.error(f"Error creating relevant equipment list: {e}")
continue continue
logger.debug(f"Relevant equipment: {pformat(relevant)}") # logger.debug(f"Relevant equipment: {pformat(relevant)}")
previous_asset = "" previous_asset = ""
for k, v in relevant.items(): for k, v in relevant.items():
logger.debug(f"Checking: {v}") # logger.debug(f"Checking: {v}")
asset = ws.cell(v['name']['row'], v['name']['column']).value asset = ws.cell(v['name']['row'], v['name']['column']).value
if not check_not_nan(asset): if not check_not_nan(asset):
asset = previous_asset asset = previous_asset
else: else:
previous_asset = asset previous_asset = asset
asset = self.get_asset_number(input=asset) asset = self.get_asset_number(input=asset)
logger.debug(f"asset: {asset}") # logger.debug(f"asset: {asset}")
eq = Equipment.query(asset_number=asset) eq = Equipment.query(asset_number=asset)
if eq is None: if eq is None:
eq = Equipment.query(name=asset) eq = Equipment.query(name=asset)
@@ -621,7 +621,7 @@ class EquipmentParser(object):
nickname=eq.nickname)) nickname=eq.nickname))
except AttributeError: except AttributeError:
logger.error(f"Unable to add {eq} to list.") logger.error(f"Unable to add {eq} to list.")
logger.debug(f"Here is the output so far: {pformat(output)}") # logger.debug(f"Here is the output so far: {pformat(output)}")
return output return output
@@ -668,7 +668,7 @@ class TipParser(object):
except (TypeError, KeyError) as e: except (TypeError, KeyError) as e:
logger.error(f"Error creating relevant equipment list: {e}") logger.error(f"Error creating relevant equipment list: {e}")
continue continue
logger.debug(f"Relevant equipment: {pformat(relevant)}") # logger.debug(f"Relevant equipment: {pformat(relevant)}")
previous_asset = "" previous_asset = ""
for k, v in relevant.items(): for k, v in relevant.items():
asset = ws.cell(v['name']['row'], v['name']['column']).value asset = ws.cell(v['name']['row'], v['name']['column']).value
@@ -680,14 +680,14 @@ class TipParser(object):
asset = previous_asset asset = previous_asset
else: else:
previous_asset = asset previous_asset = asset
logger.debug(f"asset: {asset}") # logger.debug(f"asset: {asset}")
eq = Tips.query(lot=lot, name=asset, limit=1) eq = Tips.query(lot=lot, name=asset, limit=1)
try: try:
output.append( output.append(
dict(name=eq.name, role=k, lot=lot)) dict(name=eq.name, role=k, lot=lot))
except AttributeError: except AttributeError:
logger.error(f"Unable to add {eq} to PydTips list.") logger.error(f"Unable to add {eq} to PydTips list.")
logger.debug(f"Here is the output so far: {pformat(output)}") # logger.debug(f"Here is the output so far: {pformat(output)}")
return output return output

4
src/submissions/backend/validators/__init__.py
View File

@@ -103,11 +103,11 @@ class RSLNamer(object):
regex (str): string to construct pattern regex (str): string to construct pattern
filename (str): string to be parsed filename (str): string to be parsed
""" """
logger.debug(f"Input string to be parsed: {filename}") logger.info(f"Input string to be parsed: {filename}")
if regex is None: if regex is None:
regex = BasicSubmission.construct_regex() regex = BasicSubmission.construct_regex()
else: else:
logger.debug(f"Incoming regex: {regex}") # logger.debug(f"Incoming regex: {regex}")
try: try:
regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE) regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
except re.error as e: except re.error as e:

15
src/submissions/backend/validators/pydant.py
View File

@@ -334,15 +334,20 @@ class PydEquipment(BaseModel, extra='ignore'):
Tuple[Equipment, SubmissionEquipmentAssociation]: SQL objects Tuple[Equipment, SubmissionEquipmentAssociation]: SQL objects
""" """
if isinstance(submission, str): if isinstance(submission, str):
logger.info(f"Got string, querying {submission}")
submission = BasicSubmission.query(rsl_number=submission) submission = BasicSubmission.query(rsl_number=submission)
equipment = Equipment.query(asset_number=self.asset_number) equipment = Equipment.query(asset_number=self.asset_number)
if equipment is None: if equipment is None:
logger.error("No equipment found. Returning None.")
return return
if submission is not None: if submission is not None:
# NOTE: Need to make sure the same association is not added to the submission # NOTE: Need to make sure the same association is not added to the submission
try:
assoc = SubmissionEquipmentAssociation.query(equipment_id=equipment.id, submission_id=submission.id, assoc = SubmissionEquipmentAssociation.query(equipment_id=equipment.id, submission_id=submission.id,
role=self.role, limit=1) role=self.role, limit=1)
except TypeError as e:
logger.error(f"Couldn't get association due to {e}, returning...")
return equipment, None
if assoc is None: if assoc is None:
assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment) assoc = SubmissionEquipmentAssociation(submission=submission, equipment=equipment)
process = Process.query(name=self.processes[0]) process = Process.query(name=self.processes[0])
@@ -351,8 +356,10 @@ class PydEquipment(BaseModel, extra='ignore'):
assoc.process = process assoc.process = process
assoc.role = self.role assoc.role = self.role
else: else:
logger.warning(f"Found already existing association: {assoc}")
assoc = None assoc = None
else: else:
logger.warning(f"No submission found")
assoc = None assoc = None
return equipment, assoc return equipment, assoc
@@ -608,7 +615,7 @@ class PydSubmission(BaseModel, extra='allow'):
@field_validator("contact") @field_validator("contact")
@classmethod @classmethod
def get_contact_from_org(cls, value, values): def get_contact_from_org(cls, value, values):
logger.debug(f"Checking on value: {value}") # logger.debug(f"Checking on value: {value}")
match value: match value:
case dict(): case dict():
if isinstance(value['value'], tuple): if isinstance(value['value'], tuple):
@@ -621,7 +628,7 @@ class PydSubmission(BaseModel, extra='allow'):
if check is None: if check is None:
org = Organization.query(name=values.data['submitting_lab']['value']) org = Organization.query(name=values.data['submitting_lab']['value'])
contact = org.contacts[0].name contact = org.contacts[0].name
logger.debug(f"Pulled: {contact}") # logger.debug(f"Pulled: {contact}")
if isinstance(contact, tuple): if isinstance(contact, tuple):
contact = contact[0] contact = contact[0]
return dict(value=contact, missing=True) return dict(value=contact, missing=True)
@@ -758,7 +765,7 @@ class PydSubmission(BaseModel, extra='allow'):
for tips in self.tips: for tips in self.tips:
if tips is None: if tips is None:
continue continue
logger.debug(f"Converting tips: {tips} to sql.") # logger.debug(f"Converting tips: {tips} to sql.")
try: try:
association = tips.to_sql(submission=instance) association = tips.to_sql(submission=instance)
except AttributeError: except AttributeError:

4
src/submissions/frontend/widgets/equipment_usage.py
View File

@@ -60,7 +60,7 @@ class EquipmentUsage(QDialog):
output.append(widget.parse_form()) output.append(widget.parse_form())
case _: case _:
pass pass
logger.debug(f"parsed output of Equsage form: {pformat(output)}") # logger.debug(f"parsed output of Equsage form: {pformat(output)}")
try: try:
return [item.strip() for item in output if item is not None] return [item.strip() for item in output if item is not None]
except AttributeError: except AttributeError:
@@ -169,7 +169,7 @@ class RoleComboBox(QWidget):
eq = Equipment.query(name=self.box.currentText()) eq = Equipment.query(name=self.box.currentText())
tips = [PydTips(name=item.currentText(), role=item.objectName().lstrip("tips").lstrip("_")) for item in tips = [PydTips(name=item.currentText(), role=item.objectName().lstrip("tips").lstrip("_")) for item in
self.findChildren(QComboBox) if item.objectName().startswith("tips")] self.findChildren(QComboBox) if item.objectName().startswith("tips")]
logger.debug(tips) # logger.debug(tips)
try: try:
return PydEquipment( return PydEquipment(
name=eq.name, name=eq.name,

2
src/submissions/frontend/widgets/submission_details.py
View File

@@ -84,7 +84,7 @@ class SubmissionDetails(QDialog):
if isinstance(submission, str): if isinstance(submission, str):
submission = BasicSubmission.query(rsl_plate_num=submission) submission = BasicSubmission.query(rsl_plate_num=submission)
self.base_dict = submission.to_dict(full_data=True) self.base_dict = submission.to_dict(full_data=True)
logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k == 'reagents'})}") # logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k == 'reagents'})}")
# NOTE: don't want id # NOTE: don't want id
self.base_dict = submission.finalize_details(self.base_dict) self.base_dict = submission.finalize_details(self.base_dict)
# logger.debug(f"Creating barcode.") # logger.debug(f"Creating barcode.")