Post code-cleanup, moments before disaster.
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lwark
@@ -288,8 +288,6 @@ class PydTips(BaseModel):
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tips = Tips.query(name=self.name, limit=1)
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# logger.debug(f"Tips query has yielded: {tips}")
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assoc = SubmissionTipsAssociation.query_or_create(tips=tips, submission=submission, role=self.role, limit=1)
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# if assoc is None:
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# assoc = SubmissionTipsAssociation(submission=submission, tips=tips, role_name=self.role)
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return assoc, report
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@@ -355,14 +353,13 @@ class PydEquipment(BaseModel, extra='ignore'):
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# TODO: This seems precarious. What if there is more than one process?
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# NOTE: It looks like the way fetching the processes is done in the SQL model, this shouldn't be a problem, but I'll include a failsafe.
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# NOTE: I need to find a way to filter this by the kit involved.
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if len(self.processes) > 1:
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process = Process.query(submissiontype=submission.get_submission_type(), kittype=extraction_kit, equipmentrole=self.role)
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else:
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process = Process.query(name=self.processes[0])
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if process is None:
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logger.error(f"Found unknown process: {process}.")
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logger.debug(f"Using process: {process}")
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# logger.debug(f"Using process: {process}")
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assoc.process = process
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assoc.role = self.role
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else:
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@@ -746,7 +743,16 @@ class PydSubmission(BaseModel, extra='allow'):
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output = {k: self.filter_field(k) for k in fields}
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return output
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def filter_field(self, key: str):
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def filter_field(self, key: str) -> Any:
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"""
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Attempts to get value from field dictionary
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Args:
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key (str): name of the field of interest
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Returns:
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Any (): Value found.
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"""
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item = getattr(self, key)
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match item:
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case dict():
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@@ -780,9 +786,8 @@ class PydSubmission(BaseModel, extra='allow'):
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"""
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report = Report()
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dicto = self.improved_dict()
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logger.debug(f"Pydantic submission type: {self.submission_type['value']}")
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logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
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# At this point, pcr_info is not duplicated
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# logger.debug(f"Pydantic submission type: {self.submission_type['value']}")
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# logger.debug(f"Pydantic improved_dict: {pformat(dicto)}")
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instance, result = BasicSubmission.query_or_create(submission_type=self.submission_type['value'],
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rsl_plate_num=self.rsl_plate_num['value'])
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# logger.debug(f"Created or queried instance: {instance}")
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@@ -792,8 +797,7 @@ class PydSubmission(BaseModel, extra='allow'):
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report.add_result(result)
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self.handle_duplicate_samples()
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for key, value in dicto.items():
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logger.debug(f"Checking key {key}, value {value}")
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# At this point, pcr_info is not duplicated.
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# logger.debug(f"Checking key {key}, value {value}")
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if isinstance(value, dict):
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try:
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value = value['value']
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@@ -849,8 +853,7 @@ class PydSubmission(BaseModel, extra='allow'):
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value = value
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instance.set_attribute(key=key, value=value)
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case item if item in instance.jsons:
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# At this point pcr_info is not duplicated
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logger.debug(f"Validating json value: {item} to value:{pformat(value)}")
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# logger.debug(f"Validating json value: {item} to value:{pformat(value)}")
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try:
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ii = value.items()
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except AttributeError:
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@@ -860,8 +863,7 @@ class PydSubmission(BaseModel, extra='allow'):
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value[k] = v.strftime("%Y-%m-%d %H:%M:%S")
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else:
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pass
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logger.debug(f"Setting json value: {item} to value:{pformat(value)}")
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# At this point, pcr_info is not duplicated.
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# logger.debug(f"Setting json value: {item} to value:{pformat(value)}")
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instance.set_attribute(key=key, value=value)
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case _:
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try:
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@@ -878,7 +880,6 @@ class PydSubmission(BaseModel, extra='allow'):
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continue
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else:
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logger.warning(f"{key} already == {value} so no updating.")
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logger.debug(f"Entering cost calculation for {instance}")
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try:
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instance.calculate_base_cost()
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except (TypeError, AttributeError) as e:
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@@ -937,7 +938,6 @@ class PydSubmission(BaseModel, extra='allow'):
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"/", "")
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return render
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# @report_result
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def check_kit_integrity(self, extraction_kit: str | dict | None = None, exempt: List[PydReagent] = []) -> Tuple[
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List[PydReagent], Report, List[PydReagent]]:
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"""
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@@ -1212,7 +1212,6 @@ class PydIridaControl(BaseModel, extra='ignore'):
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contains: list | dict #: unstructured hashes in contains.tsv for each organism
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matches: list | dict #: unstructured hashes in matches.tsv for each organism
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kraken: list | dict #: unstructured output from kraken_report
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# subtype: str #: EN-NOS, MCS-NOS, etc
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subtype: Literal["ATCC49226", "ATCC49619", "EN-NOS", "EN-SSTI", "MCS-NOS", "MCS-SSTI", "SN-NOS", "SN-SSTI"]
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refseq_version: str #: version of refseq used in fastq parsing
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kraken2_version: str
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@@ -1264,7 +1263,6 @@ class PydProcess(BaseModel, extra="allow"):
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instance = Process.query(name=self.name)
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if not instance:
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instance = Process()
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# dicto = instance.omnigui_instance_dict
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fields = [item for item in self.model_fields]
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for field in fields:
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logger.debug(f"Field: {field}")
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@@ -1315,5 +1313,3 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
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field_value = getattr(self, field)
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self.instance.__setattr__(field, field_value)
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return self.instance
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