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

Writer improvements.

Browse Source
This commit is contained in:
lwark
2025-07-24 11:16:37 -05:00
parent 1463cf9d2d
commit 2c6a8c4cc7
16 changed files with 85 additions and 32 deletions
Download Patch File Download Diff File Expand all files Collapse all files

3
src/submissions/backend/db/models/__init__.py
View File

@@ -644,7 +644,7 @@ class BaseClass(Base):
return output return output
@classmethod @classmethod
def clean_details_dict(cls, dictionary): def clean_details_for_render(cls, dictionary):
output = {} output = {}
for k, value in dictionary.items(): for k, value in dictionary.items():
match value: match value:
@@ -668,7 +668,6 @@ class BaseClass(Base):
case _: case _:
pass pass
output[k] = value output[k] = value
return output return output

6
src/submissions/backend/db/models/kits.py
View File

@@ -1572,7 +1572,7 @@ class Procedure(BaseClass):
for reagent in output.reagent: for reagent in output.reagent:
match reagent: match reagent:
case dict(): case dict():
reagent['reagentrole'] = next((reagentrole.name for reagentrole in self.kittype.reagentrole if reagentrole == reagent['reagentrole']), None) # reagent['reagentrole'] = next((reagentrole.name for reagentrole in self.kittype.reagentrole if reagentrole == reagent['reagentrole']), None)
reagents.append(PydReagent(**reagent)) reagents.append(PydReagent(**reagent))
case PydReagent(): case PydReagent():
reagents.append(reagent) reagents.append(reagent)
@@ -2067,10 +2067,12 @@ class ProcedureReagentAssociation(BaseClass):
# NOTE: Figure out how to merge the misc_info if doing .update instead. # NOTE: Figure out how to merge the misc_info if doing .update instead.
relevant = {k: v for k, v in output.items() if k not in ['reagent']} relevant = {k: v for k, v in output.items() if k not in ['reagent']}
output = output['reagent'].details_dict() output = output['reagent'].details_dict()
misc = output['misc_info'] misc = output['misc_info']
output.update(relevant) output.update(relevant)
output['reagentrole'] = self.reagentrole
output['misc_info'] = misc output['misc_info'] = misc
# output['results'] = [result.details_dict() for result in output['results']] logger.debug(f"Output: {pformat(output)}")
return output return output
def delete(self, **kwargs): def delete(self, **kwargs):

6
src/submissions/backend/db/models/submissions.py
View File

@@ -438,7 +438,10 @@ class Run(BaseClass, LogMixin):
if self._started_date: if self._started_date:
return self._started_date return self._started_date
else: else:
value = min([proc.started_date for proc in self.procedure]) try:
value = min([proc.started_date for proc in self.procedure])
except ValueError:
value = datetime.now()
return value return value
@started_date.setter @started_date.setter
@@ -2191,6 +2194,7 @@ class ProcedureSampleAssociation(BaseClass):
sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True) #: id of associated equipment sample_id = Column(INTEGER, ForeignKey("_sample.id"), primary_key=True) #: id of associated equipment
row = Column(INTEGER) row = Column(INTEGER)
column = Column(INTEGER) column = Column(INTEGER)
plate_rank = Column(INTEGER)
procedure = relationship(Procedure, procedure = relationship(Procedure,
back_populates="proceduresampleassociation") #: associated procedure back_populates="proceduresampleassociation") #: associated procedure

6
src/submissions/backend/excel/parsers/clientsubmission_parser.py
View File

@@ -78,7 +78,7 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
default_range_dict = [dict( default_range_dict = [dict(
start_row=2, start_row=2,
end_row=18, end_row=16,
key_column=1, key_column=1,
value_column=2, value_column=2,
sheet="Sample List" sheet="Sample List"
@@ -117,8 +117,8 @@ class ClientSubmissionSampleParser(DefaultTABLEParser, SubmissionTyperMixin):
pyd_name = "PydSample" pyd_name = "PydSample"
default_range_dict = [dict( default_range_dict = [dict(
header_row=19, header_row=18,
end_row=115, end_row=114,
sheet="Sample List" sheet="Sample List"
)] )]

9
src/submissions/backend/excel/parsers/results_parsers/pcr_results_parser.py
View File

@@ -61,7 +61,7 @@ class PCRSampleParser(DefaultTABLEParser):
yield {sample: multi} yield {sample: multi}
def to_pydantic(self): def to_pydantic(self):
logger.debug(f"running to pydantic") logger.debug("running to pydantic")
for item in self.parsed_info: for item in self.parsed_info:
# sample_obj = Sample.query(sample_id=list(item.keys())[0]) # sample_obj = Sample.query(sample_id=list(item.keys())[0])
# NOTE: Ensure that only samples associated with the procedure are used. # NOTE: Ensure that only samples associated with the procedure are used.
@@ -70,12 +70,15 @@ class PCRSampleParser(DefaultTABLEParser):
(sample for sample in self.procedure.sample if sample.sample_id == list(item.keys())[0])) (sample for sample in self.procedure.sample if sample.sample_id == list(item.keys())[0]))
except StopIteration: except StopIteration:
continue continue
logger.debug(f"Sample object {sample_obj}") # logger.debug(f"Sample object {sample_obj}")
assoc = ProcedureSampleAssociation.query(sample=sample_obj, procedure=self.procedure) assoc = ProcedureSampleAssociation.query(sample=sample_obj, procedure=self.procedure)
if assoc and not isinstance(assoc, list): if assoc and not isinstance(assoc, list):
output = self._pyd_object(results=list(item.values())[0], parent=assoc) output = self._pyd_object(results=list(item.values())[0], parent=assoc)
output.result_type = "PCR" output.result_type = "PCR"
del output.result['result_type'] try:
del output.result['result_type']
except KeyError:
pass
yield output yield output
else: else:
continue continue

13
src/submissions/backend/excel/writers/__init__.py
View File

@@ -128,6 +128,7 @@ class DefaultTABLEWriter(DefaultWriter):
for column in column_names: for column in column_names:
setattr(sample, column[0], "") setattr(sample, column[0], "")
sample.submission_rank = iii sample.submission_rank = iii
sample.plate_rank = iii
# logger.debug(f"Appending {sample.sample_id}") # logger.debug(f"Appending {sample.sample_id}")
# logger.debug(f"Iterator now: {[item.submission_rank for item in iterator]}") # logger.debug(f"Iterator now: {[item.submission_rank for item in iterator]}")
output_samples.append(sample) output_samples.append(sample)
@@ -137,7 +138,7 @@ class DefaultTABLEWriter(DefaultWriter):
workbook = super().write_to_workbook(workbook=workbook) workbook = super().write_to_workbook(workbook=workbook)
for rng in self.range_dict: for rng in self.range_dict:
list_worksheet = workbook[rng['sheet']] list_worksheet = workbook[rng['sheet']]
column_names = [(item.value.lower().replace(" ", "_"), item.column) for item in list_worksheet[rng['header_row']] if item.value] column_names = [(str(item.value).lower().replace(" ", "_"), item.column) for item in list_worksheet[rng['header_row']] if item.value]
for iii, object in enumerate(self.pydant_obj, start=1): for iii, object in enumerate(self.pydant_obj, start=1):
# logger.debug(f"Writing object: {object}") # logger.debug(f"Writing object: {object}")
write_row = rng['header_row'] + iii write_row = rng['header_row'] + iii
@@ -156,6 +157,16 @@ class DefaultTABLEWriter(DefaultWriter):
list_worksheet.cell(row=write_row, column=write_column, value=self.stringify_value(value)) list_worksheet.cell(row=write_row, column=write_column, value=self.stringify_value(value))
return workbook return workbook
@classmethod
def construct_column_names(cls, column_item):
column = column_item.column
match column_item.value:
case str():
value = column_item.value.lower().replace(" ", "_")
case _:
value = column_item.value
return value, column
from .clientsubmission_writer import ClientSubmissionInfoWriter, ClientSubmissionSampleWriter from .clientsubmission_writer import ClientSubmissionInfoWriter, ClientSubmissionSampleWriter

7
src/submissions/backend/excel/writers/clientsubmission_writer.py
View File

@@ -47,15 +47,18 @@ class ClientSubmissionSampleWriter(DefaultTABLEWriter):
def write_to_workbook(self, workbook: Workbook) -> Workbook: def write_to_workbook(self, workbook: Workbook) -> Workbook:
workbook = super().write_to_workbook(workbook=workbook) workbook = super().write_to_workbook(workbook=workbook)
# logger.debug(f"\n\nHello from {self.__class__.__name__} with range_dict: {pformat(self.range_dict)}")
for rng in self.range_dict: for rng in self.range_dict:
list_worksheet = workbook[rng['sheet']] list_worksheet = workbook[rng['sheet']]
row_count = self.get_row_count(list_worksheet, rng) row_count = self.get_row_count(list_worksheet, rng)
column_names = [(item.value.lower().replace(" ", "_"), item.column) for item in list_worksheet[rng['header_row']] if item.value] column_names = [(str(item.value).lower().replace(" ", "_"), item.column) for item in list_worksheet[rng['header_row']] if item.value]
samples = self.pad_samples_to_length(row_count=row_count, column_names=column_names) samples = self.pad_samples_to_length(row_count=row_count, column_names=column_names)
# logger.debug(f"Samples: {pformat(samples)}")
for sample in samples: for sample in samples:
# logger.debug(f"Writing sample: {sample}")
write_row = rng['header_row'] + sample.submission_rank write_row = rng['header_row'] + sample.submission_rank
# logger.debug(f"Writing sample: {sample} to row {write_row}")
for column in column_names: for column in column_names:
# logger.debug(f"At column {column}")
if column[0].lower() in ["well", "row", "column"]: if column[0].lower() in ["well", "row", "column"]:
continue continue
write_column = column[1] write_column = column[1]

8
src/submissions/backend/excel/writers/procedure_writers/__init__.py
View File

@@ -1,5 +1,6 @@
from __future__ import annotations from __future__ import annotations
import logging import logging
import sys
from pprint import pformat from pprint import pformat
from openpyxl.workbook import Workbook from openpyxl.workbook import Workbook
@@ -24,7 +25,7 @@ class ProcedureInfoWriter(DefaultKEYVALUEWriter):
'procedurereagentassociation', 'proceduresampleassociation', 'proceduretipsassociation', 'reagent', 'reagentrole', 'procedurereagentassociation', 'proceduresampleassociation', 'proceduretipsassociation', 'reagent', 'reagentrole',
'results', 'sample', 'tips'] 'results', 'sample', 'tips']
self.fill_dictionary = {k: v for k, v in self.fill_dictionary.items() if k not in exclude} self.fill_dictionary = {k: v for k, v in self.fill_dictionary.items() if k not in exclude}
logger.debug(pformat(self.fill_dictionary)) # logger.debug(pformat(self.fill_dictionary))
for rng in self.range_dict: for rng in self.range_dict:
if "sheet" not in rng or rng['sheet'] == "": if "sheet" not in rng or rng['sheet'] == "":
rng['sheet'] = f"{pydant_obj.proceduretype.name} Quality" rng['sheet'] = f"{pydant_obj.proceduretype.name} Quality"
@@ -79,11 +80,14 @@ class ProcedureSampleWriter(DefaultTABLEWriter):
column_names = [(item.value.lower().replace(" ", "_"), item.column) for item in column_names = [(item.value.lower().replace(" ", "_"), item.column) for item in
list_worksheet[rng['header_row']] if item.value] list_worksheet[rng['header_row']] if item.value]
samples = self.pad_samples_to_length(row_count=row_count, column_names=column_names) samples = self.pad_samples_to_length(row_count=row_count, column_names=column_names)
samples = sorted(samples, key=lambda x: x.plate_rank)
# samples = self.pydant_obj # samples = self.pydant_obj
# logger.debug(f"Samples: {[item.submission_rank for item in samples]}") # logger.debug(f"Samples: {[item.submission_rank for item in samples]}")
for sample in samples: for sample in samples:
# logger.debug(f"Writing sample: {sample}") # logger.debug(f"Writing sample: {sample}")
write_row = rng['header_row'] + sample.submission_rank if sample.row == 0 or sample.column == 0:
continue
write_row = rng['header_row'] + sample.plate_rank
for column in column_names: for column in column_names:
if column[0].lower() in ["well"]:#, "row", "column"]: if column[0].lower() in ["well"]:#, "row", "column"]:
continue continue

11
src/submissions/backend/excel/writers/results_writers/pcr_results_writer.py
View File

@@ -23,7 +23,7 @@ class PCRInfoWriter(DefaultKEYVALUEWriter):
def write_to_workbook(self, workbook: Workbook) -> Workbook: def write_to_workbook(self, workbook: Workbook) -> Workbook:
worksheet = workbook[f"{self.proceduretype.name} Results"] worksheet = workbook[f"{self.proceduretype.name} Results"]
for key, value in self.fill_dictionary['result'].items(): for key, value in self.fill_dictionary['result'].items():
logger.debug(f"Filling in {key} with {value}") # logger.debug(f"Filling in {key} with {value}")
worksheet.cell(value['location']['row'], value['location']['key_column'], value=key.replace("_", " ").title()) worksheet.cell(value['location']['row'], value['location']['key_column'], value=key.replace("_", " ").title())
worksheet.cell(value['location']['row'], value['location']['value_column'], value=value['value']) worksheet.cell(value['location']['row'], value['location']['value_column'], value=value['value'])
return workbook return workbook
@@ -41,7 +41,7 @@ class PCRSampleWriter(DefaultTABLEWriter):
columns.append((iii, header)) columns.append((iii, header))
columns = sorted(columns, key=lambda x: x[0]) columns = sorted(columns, key=lambda x: x[0])
columns = proto_columns + columns columns = proto_columns + columns
logger.debug(columns) # logger.debug(columns)
all_results = flatten_list([[item for item in self.rearrange_results(result)] for result in self.pydant_obj]) all_results = flatten_list([[item for item in self.rearrange_results(result)] for result in self.pydant_obj])
if len(all_results) > 0 : if len(all_results) > 0 :
worksheet.cell(row=header_row, column=1, value="Sample") worksheet.cell(row=header_row, column=1, value="Sample")
@@ -58,6 +58,8 @@ class PCRSampleWriter(DefaultTABLEWriter):
@classmethod @classmethod
def rearrange_results(cls, result) -> Generator[dict, None, None]: def rearrange_results(cls, result) -> Generator[dict, None, None]:
for target, values in result.result.items(): for target, values in result.result.items():
if not isinstance(values, dict):
continue
values['target'] = target values['target'] = target
values['sample'] = result.sample_id values['sample'] = result.sample_id
yield values yield values
@@ -66,9 +68,12 @@ class PCRSampleWriter(DefaultTABLEWriter):
def column_headers(self): def column_headers(self):
output = [] output = []
for item in self.pydant_obj: for item in self.pydant_obj:
logger.debug(item) # logger.debug(item)
dicto: dict = item.result dicto: dict = item.result
for value in dicto.values(): for value in dicto.values():
if not isinstance(value, dict):
# logger.debug(f"Will not include {value} in column headers.")
continue
for key in value.keys(): for key in value.keys():
output.append(key) output.append(key)
return sorted(list(set(output))) return sorted(list(set(output)))

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

@@ -24,10 +24,10 @@ class DefaultManager(object):
self.input_object = input_object self.input_object = input_object
self.pyd = self.parse() self.pyd = self.parse()
case x if issubclass(input_object.__class__, PydBaseClass): case x if issubclass(input_object.__class__, PydBaseClass):
logger.debug("Subclass of PydBaseClass") # logger.debug("Subclass of PydBaseClass")
self.pyd = input_object self.pyd = input_object
case x if issubclass(input_object.__class__, BaseClass): case x if issubclass(input_object.__class__, BaseClass):
logger.debug("Subclass of BaseClass") # logger.debug("Subclass of BaseClass")
self.pyd = input_object.to_pydantic() self.pyd = input_object.to_pydantic()
case _: case _:
self.input_object = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent)) self.input_object = select_open_file(file_extension="xlsx", obj=get_application_from_parent(parent))

4
src/submissions/backend/managers/procedures.py
View File

@@ -82,14 +82,14 @@ class DefaultProcedureManager(DefaultManager):
sample_writer = procedure_writers.ProcedureSampleWriter sample_writer = procedure_writers.ProcedureSampleWriter
self.sample_writer = sample_writer(pydant_obj=self.pyd, range_dict=self.proceduretype.sample_map) self.sample_writer = sample_writer(pydant_obj=self.pyd, range_dict=self.proceduretype.sample_map)
workbook = self.sample_writer.write_to_workbook(workbook) workbook = self.sample_writer.write_to_workbook(workbook)
logger.debug(self.pyd.result) # logger.debug(self.pyd.result)
# TODO: Find way to group results by result_type. # TODO: Find way to group results by result_type.
for result in self.pyd.result: for result in self.pyd.result:
Writer = getattr(results_writers, f"{result.result_type}InfoWriter") Writer = getattr(results_writers, f"{result.result_type}InfoWriter")
res_info_writer = Writer(pydant_obj=result, proceduretype=self.proceduretype) res_info_writer = Writer(pydant_obj=result, proceduretype=self.proceduretype)
workbook = res_info_writer.write_to_workbook(workbook=workbook) workbook = res_info_writer.write_to_workbook(workbook=workbook)
# sample_results = [sample.result for sample in self.pyd.sample] # sample_results = [sample.result for sample in self.pyd.sample]
logger.debug(pformat(self.pyd.sample_results)) # logger.debug(pformat(self.pyd.sample_results))
Writer = getattr(results_writers, "PCRSampleWriter") Writer = getattr(results_writers, "PCRSampleWriter")
res_sample_writer = Writer(pydant_obj=self.pyd.sample_results, proceduretype=self.proceduretype) res_sample_writer = Writer(pydant_obj=self.pyd.sample_results, proceduretype=self.proceduretype)
workbook = res_sample_writer.write_to_workbook(workbook=workbook) workbook = res_sample_writer.write_to_workbook(workbook=workbook)

2
src/submissions/backend/managers/runs.py
View File

@@ -20,7 +20,7 @@ class DefaultRunManager(DefaultManager):
clientsubmission = DefaultClientSubmissionManager(parent=self.parent, input_object=self.pyd.clientsubmission, submissiontype=self.pyd.clientsubmission.submissiontype) clientsubmission = DefaultClientSubmissionManager(parent=self.parent, input_object=self.pyd.clientsubmission, submissiontype=self.pyd.clientsubmission.submissiontype)
workbook = clientsubmission.write() workbook = clientsubmission.write()
for procedure in self.pyd.procedure: for procedure in self.pyd.procedure:
logger.debug(f"Running procedure: {pformat(procedure.__dict__)}") # logger.debug(f"Running procedure: {pformat(procedure.__dict__)}")
procedure = DefaultProcedureManager(proceduretype=procedure.proceduretype, parent=self.parent, input_object=procedure) procedure = DefaultProcedureManager(proceduretype=procedure.proceduretype, parent=self.parent, input_object=procedure)
wb: Workbook = procedure.write() wb: Workbook = procedure.write()
for sheetname in wb.sheetnames: for sheetname in wb.sheetnames:

24
src/submissions/backend/validators/pydant.py
View File

@@ -1449,7 +1449,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
def update_samples(self, sample_list: List[dict]): def update_samples(self, sample_list: List[dict]):
logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}") logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
for sample_dict in sample_list: for iii, sample_dict in enumerate(sample_list, start=1):
if sample_dict['sample_id'].startswith("blank_"): if sample_dict['sample_id'].startswith("blank_"):
sample_dict['sample_id'] = "" sample_dict['sample_id'] = ""
row, column = self.proceduretype.ranked_plate[sample_dict['index']] row, column = self.proceduretype.ranked_plate[sample_dict['index']]
@@ -1467,11 +1467,12 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
except StopIteration: except StopIteration:
logger.error(f"Couldn't find sample: {pformat(sample_dict)}") logger.error(f"Couldn't find sample: {pformat(sample_dict)}")
continue continue
logger.debug(f"Sample of interest: {sample.improved_dict()}")
sample.sample_id = sample_dict['sample_id'] sample.sample_id = sample_dict['sample_id']
sample.well_id = sample_dict['sample_id'] sample.well_id = sample_dict['sample_id']
sample.row = row sample.row = row
sample.column = column sample.column = column
sample.plate_rank = sample_dict['index']
logger.debug(f"Sample of interest: {sample.improved_dict()}")
# logger.debug(f"Updated samples:\n{pformat(self.sample)}") # logger.debug(f"Updated samples:\n{pformat(self.sample)}")
def update_reagents(self, reagentrole: str, name: str, lot: str, expiry: str): def update_reagents(self, reagentrole: str, name: str, lot: str, expiry: str):
@@ -1502,6 +1503,14 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
sql = super().to_sql() sql = super().to_sql()
logger.debug(f"Initial PYD: {pformat(self.__dict__)}") logger.debug(f"Initial PYD: {pformat(self.__dict__)}")
# sql.results = [result.to_sql() for result in self.results] # sql.results = [result.to_sql() for result in self.results]
if isinstance(self.name, dict):
sql.name = self.name['value']
else:
sql.name = self.name
if isinstance(self.technician, dict):
sql.technician = self.technician['value']
else:
sql.technician = self.technician
sql.repeat = self.repeat sql.repeat = self.repeat
if sql.repeat: if sql.repeat:
regex = re.compile(r".*\dR\d$") regex = re.compile(r".*\dR\d$")
@@ -1563,7 +1572,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
logger.debug(f"sample {sample_sql} found in {sql.run.sample}") logger.debug(f"sample {sample_sql} found in {sql.run.sample}")
if sample_sql not in sql.sample: if sample_sql not in sql.sample:
proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql, proc_assoc = ProcedureSampleAssociation(new_id=assoc_id_range[iii], procedure=sql, sample=sample_sql,
row=sample.row, column=sample.column) row=sample.row, column=sample.column, plate_rank=sample.plate_rank)
if self.kittype['value'] not in ["NA", None, ""]: if self.kittype['value'] not in ["NA", None, ""]:
kittype = KitType.query(name=self.kittype['value'], limit=1) kittype = KitType.query(name=self.kittype['value'], limit=1)
if kittype: if kittype:
@@ -1675,6 +1684,13 @@ class PydClientSubmission(PydBaseClass):
value['value'] = "NA" value['value'] = "NA"
return value return value
@field_validator("comment", mode="before")
@classmethod
def convert_comment_string(cls, value):
if isinstance(value, str):
value = dict(value=value, missing=True)
return value
def to_form(self, parent: QWidget, samples: List = [], disable: list | None = None): def to_form(self, parent: QWidget, samples: List = [], disable: list | None = None):
""" """
Converts this instance into a frontend.widgets.submission_widget.SubmissionFormWidget Converts this instance into a frontend.widgets.submission_widget.SubmissionFormWidget
@@ -1763,6 +1779,8 @@ class PydResults(PydBaseClass, arbitrary_types_allowed=True):
value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S") value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
case datetime(): case datetime():
pass pass
case date():
value = datetime.combine(value, datetime.max.time())
case _: case _:
value = datetime.now() value = datetime.now()
return value return value

8
src/submissions/frontend/widgets/procedure_creation.py
View File

@@ -15,7 +15,7 @@ from PyQt6.QtGui import QContextMenuEvent, QAction
from PyQt6.QtWebChannel import QWebChannel from PyQt6.QtWebChannel import QWebChannel
from PyQt6.QtWebEngineWidgets import QWebEngineView from PyQt6.QtWebEngineWidgets import QWebEngineView
from PyQt6.QtWidgets import QDialog, QGridLayout, QMenu, QDialogButtonBox from PyQt6.QtWidgets import QDialog, QGridLayout, QMenu, QDialogButtonBox
from typing import TYPE_CHECKING, Any from typing import TYPE_CHECKING, Any, List
if TYPE_CHECKING: if TYPE_CHECKING:
from backend.db.models import Run, Procedure from backend.db.models import Run, Procedure
@@ -36,9 +36,12 @@ class ProcedureCreation(QDialog):
self.setWindowTitle(f"New {self.proceduretype.name} for {self.run.rsl_plate_number}") self.setWindowTitle(f"New {self.proceduretype.name} for {self.run.rsl_plate_number}")
# self.created_procedure = self.proceduretype.construct_dummy_procedure(run=self.run) # self.created_procedure = self.proceduretype.construct_dummy_procedure(run=self.run)
self.procedure.update_kittype_reagentroles(kittype=self.procedure.possible_kits[0]) self.procedure.update_kittype_reagentroles(kittype=self.procedure.possible_kits[0])
# self.created_procedure.samples = self.run.constuct_sample_dicts_for_proceduretype(proceduretype=self.proceduretype) # self.created_procedure.samples = self.run.constuct_sample_dicts_for_proceduretype(proceduretype=self.proceduretype)
# logger.debug(f"Samples to map\n{pformat(self.created_procedure.samples)}") # logger.debug(f"Samples to map\n{pformat(self.created_procedure.samples)}")
self.plate_map = self.proceduretype.construct_plate_map(sample_dicts=self.procedure.sample) self.plate_map = self.proceduretype.construct_plate_map(sample_dicts=self.procedure.sample)
self.procedure.update_samples(sample_list=[dict(sample_id=sample.sample_id, index=iii) for iii, sample in
enumerate(self.procedure.sample, start=1)])
# logger.debug(f"Plate map: {self.plate_map}") # logger.debug(f"Plate map: {self.plate_map}")
# logger.debug(f"Created dummy: {self.created_procedure}") # logger.debug(f"Created dummy: {self.created_procedure}")
self.app = get_application_from_parent(parent) self.app = get_application_from_parent(parent)
@@ -64,6 +67,7 @@ class ProcedureCreation(QDialog):
self.buttonBox.rejected.connect(self.reject) self.buttonBox.rejected.connect(self.reject)
self.layout.addWidget(self.buttonBox, 11, 1, 1, 1) self.layout.addWidget(self.buttonBox, 11, 1, 1, 1)
def set_html(self): def set_html(self):
from .equipment_usage_2 import EquipmentUsage from .equipment_usage_2 import EquipmentUsage
logger.debug(f"Edit: {self.edit}") logger.debug(f"Edit: {self.edit}")
@@ -151,7 +155,7 @@ class ProcedureCreation(QDialog):
self.set_html() self.set_html()
@pyqtSlot(list) @pyqtSlot(list)
def rearrange_plate(self, sample_list: list): def rearrange_plate(self, sample_list: List[dict]):
self.procedure.update_samples(sample_list=sample_list) self.procedure.update_samples(sample_list=sample_list)
@pyqtSlot(str) @pyqtSlot(str)

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

@@ -55,7 +55,7 @@ class SubmissionDetails(QDialog):
self.webview.page().setWebChannel(self.channel) self.webview.page().setWebChannel(self.channel)
def object_details(self, object): def object_details(self, object):
details = object.clean_details_dict(object.details_dict()) details = object.clean_details_for_render(object.details_dict())
template = object.details_template template = object.details_template
template_path = Path(template.environment.loader.__getattribute__("searchpath")[0]) template_path = Path(template.environment.loader.__getattribute__("searchpath")[0])
with open(template_path.joinpath("css", "styles.css"), "r") as f: with open(template_path.joinpath("css", "styles.css"), "r") as f:

4
src/submissions/templates/procedure_details.html
View File

@@ -49,8 +49,8 @@
{% if procedure['results'] %} {% if procedure['results'] %}
<button type="button"><h3><u>Results:</u></h3></button> <button type="button"><h3><u>Results:</u></h3></button>
{% for result in procedure['results'] %} {% for result in procedure['results'] %}
<p>{% for k, v in result['result'].items() %} <p>{% for key, value in result['result'].items() %}
<b>{{ key | replace("_", " ") | title | replace("Rsl", "RSL") }}:</b> {{ value }}<br> <b>{{ key | replace("_", " ") | title | replace("Rsl", "RSL") }}:</b> {{ value['value'] }}<br>
{% endfor %}</p> {% endfor %}</p>
{% endfor %} {% endfor %}
{% endif %} {% endif %}