Converted client manager to new Omni pydantic version.
This commit is contained in:
lwark
@@ -3,6 +3,7 @@ Models for the main submission and sample types.
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"""
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from __future__ import annotations
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import itertools
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import pickle
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from copy import deepcopy
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from getpass import getuser
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@@ -12,6 +13,8 @@ from zipfile import ZipFile, BadZipfile
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from tempfile import TemporaryDirectory, TemporaryFile
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from operator import itemgetter
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from pprint import pformat
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from pandas import DataFrame
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from sqlalchemy.ext.hybrid import hybrid_property
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from . import BaseClass, Reagent, SubmissionType, KitType, Organization, Contact, LogMixin, SubmissionReagentAssociation
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from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, JSON, FLOAT, case, func
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@@ -287,6 +290,7 @@ class BasicSubmission(BaseClass, LogMixin):
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Constructs dictionary used in submissions summary
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Args:
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expand (bool, optional): indicates if generators to be expanded. Defaults to False.
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report (bool, optional): indicates if to be used for a report. Defaults to False.
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full_data (bool, optional): indicates if sample dicts to be constructed. Defaults to False.
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backup (bool, optional): passed to adjust_to_dict_samples. Defaults to False.
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@@ -393,6 +397,33 @@ class BasicSubmission(BaseClass, LogMixin):
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output["completed_date"] = self.completed_date
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return output
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@classmethod
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def archive_submissions(cls, start_date: date | datetime | str | int | None = None,
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end_date: date | datetime | str | int | None = None,
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submissiontype: List[str] | None = None):
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if submissiontype:
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if isinstance(submissiontype, str):
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submissiontype = [submissiontype]
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query_out = []
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for sub_type in submissiontype:
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subs = cls.query(page_size=0, start_date=start_date, end_date=end_date, submissiontype=sub_type)
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# logger.debug(f"Sub results: {subs}")
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query_out.append(subs)
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query_out = list(itertools.chain.from_iterable(query_out))
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else:
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query_out = cls.query(page_size=0, start_date=start_date, end_date=end_date)
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records = []
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for sub in query_out:
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output = sub.to_dict(full_data=True)
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for k, v in output.items():
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if isinstance(v, types.GeneratorType):
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output[k] = [item for item in v]
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records.append(output)
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df = DataFrame.from_records(records)
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df.sort_values(by="id", inplace=True)
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df.set_index("id", inplace=True)
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return df
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@property
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def column_count(self) -> int:
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"""
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@@ -590,61 +621,18 @@ class BasicSubmission(BaseClass, LogMixin):
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except AttributeError as e:
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logger.error(f"Could not set {self} attribute {key} to {value} due to \n{e}")
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# def update_subsampassoc(self, sample: BasicSample, input_dict: dict) -> SubmissionSampleAssociation:
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# """
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# Update a joined submission sample association.
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#
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# Args:
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# sample (BasicSample): Associated sample.
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# input_dict (dict): values to be updated
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#
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# Returns:
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# SubmissionSampleAssociation: Updated association
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# """
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# try:
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# logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
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# assoc = next((item for item in self.submission_sample_associations
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# if item.sample == sample and
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# item.row == input_dict['row'] and
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# item.column == input_dict['column']))
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# logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
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# except StopIteration:
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# report = Report()
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# report.add_result(
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# Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
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# return report
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# for k, v in input_dict.items():
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# try:
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# # logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
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# setattr(assoc, k, v)
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# # NOTE: for some reason I don't think assoc.__setattr__(k, v) works here.
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# except AttributeError:
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# logger.error(f"Can't set {k} to {v}")
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# return assoc
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def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
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"""
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Update a joined submission sample association.
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Args:
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sample (BasicSample): Associated sample.
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input_dict (dict): values to be updated
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assoc (SubmissionSampleAssociation): Sample association to be updated.
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input_dict (dict): updated values to insert.
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Returns:
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SubmissionSampleAssociation: Updated association
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"""
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# try:
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# logger.debug(f"Searching for sample {sample} at column {input_dict['column']} and row {input_dict['row']}")
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# assoc = next((item for item in self.submission_sample_associations
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# if item.sample == sample and
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# item.row == input_dict['row'] and
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# item.column == input_dict['column']))
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# logger.debug(f"Found assoc {pformat(assoc.__dict__)}")
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# except StopIteration:
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# report = Report()
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# report.add_result(
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# Result(msg=f"Couldn't find submission sample association for {sample.submitter_id}", status="Warning"))
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# return report
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# NOTE: No longer searches for association here, done in caller function
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for k, v in input_dict.items():
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try:
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# logger.debug(f"Setting assoc {assoc} with key {k} to value {v}")
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@@ -771,8 +759,8 @@ class BasicSubmission(BaseClass, LogMixin):
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return regex
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@classmethod
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def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | None = None,
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attrs: dict | None = None) -> BasicSubmission:
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def find_polymorphic_subclass(cls, polymorphic_identity: str | SubmissionType | list | None = None,
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attrs: dict | None = None) -> BasicSubmission | List[BasicSubmission]:
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"""
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Find subclass based on polymorphic identity or relevant attributes.
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@@ -795,6 +783,13 @@ class BasicSubmission(BaseClass, LogMixin):
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except Exception as e:
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logger.error(
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f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
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case list():
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output = []
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for identity in polymorphic_identity:
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if isinstance(identity, SubmissionType):
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identity = polymorphic_identity.name
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output.append(cls.__mapper__.polymorphic_map[identity].class_)
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return output
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case _:
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pass
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if attrs and any([not hasattr(cls, attr) for attr in attrs.keys()]):
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@@ -1855,18 +1850,6 @@ class Wastewater(BasicSubmission):
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result = assoc.save()
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if result:
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report.add_result(result)
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# for sample in self.samples:
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# logger.debug(f"Checking pcr_samples for {sample.rsl_number}, {sample.ww_full_sample_id}")
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# try:
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# # NOTE: Fix for ENs which have no rsl_number...
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# sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
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# logger.debug(f"Found sample {sample_dict} at index {pcr_samples.index(sample_dict)}: {pcr_samples[pcr_samples.index(sample_dict)]}")
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# except StopIteration:
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# logger.error(f"Couldn't find {sample} in the Parser samples")
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# continue
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# assoc = self.update_subsampassoc(sample=sample, input_dict=sample_dict)
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# result = assoc.save()
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# report.add_result(result)
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controltype = ControlType.query(name="PCR Control")
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submitted_date = datetime.strptime(" ".join(parser.pcr_info['run_start_date/time'].split(" ")[:-1]),
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"%Y-%m-%d %I:%M:%S %p")
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@@ -1880,35 +1863,6 @@ class Wastewater(BasicSubmission):
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new_control.save()
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return report
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# def update_subsampassoc(self, assoc: SubmissionSampleAssociation, input_dict: dict) -> SubmissionSampleAssociation:
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# """
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# Updates a joined submission sample association by assigning ct values to n1 or n2 based on alphabetical sorting.
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#
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# Args:
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# sample (BasicSample): Associated sample.
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# input_dict (dict): values to be updated
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#
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# Returns:
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# SubmissionSampleAssociation: Updated association
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# """
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# # logger.debug(f"Input dict: {pformat(input_dict)}")
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# #
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# assoc = super().update_subsampassoc(assoc=assoc, input_dict=input_dict)
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# # targets = {k: input_dict[k] for k in sorted(input_dict.keys()) if k.startswith("ct_")}
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# # assert 0 < len(targets) <= 2
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# # for k, v in targets.items():
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# # # logger.debug(f"Setting sample {sample} with key {k} to value {v}")
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# # # update_key = f"ct_n{i}"
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# # current_value = getattr(assoc, k)
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# # logger.debug(f"Current value came back as: {current_value}")
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# # if current_value is None:
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# # setattr(assoc, k, v)
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# # else:
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# # logger.debug(f"Have a value already, {current_value}... skipping.")
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# if assoc.column == 3:
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# logger.debug(f"Final association for association {assoc}:\n{pformat(assoc.__dict__)}")
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# return assoc
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class WastewaterArtic(BasicSubmission):
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"""
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@@ -2196,14 +2150,14 @@ class WastewaterArtic(BasicSubmission):
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# logger.debug(processed)
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# NOTE: Remove brackets at end
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processed = re.sub(r"\(.*\)$", "", processed).strip()
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logger.debug(processed)
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# logger.debug(processed)
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processed = re.sub(r"-RPT", "", processed, flags=re.IGNORECASE)
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# NOTE: Remove any non-R letters at end.
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processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
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logger.debug(processed)
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# logger.debug(processed)
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# NOTE: Remove trailing '-' if any
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processed = processed.strip("-")
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logger.debug(processed)
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# logger.debug(processed)
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try:
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plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
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processed = rreplace(processed, plate_num, "")
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@@ -2221,20 +2175,20 @@ class WastewaterArtic(BasicSubmission):
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plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
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except AttributeError:
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logger.error(f"Problem re-evaluating plate number for {processed}")
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logger.debug(processed)
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# logger.debug(processed)
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# NOTE: Remove any redundant -digits
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processed = re.sub(r"-\d$", "", processed)
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logger.debug(processed)
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# logger.debug(processed)
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day = re.search(r"\d{2}$", processed).group()
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processed = rreplace(processed, day, "")
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logger.debug(processed)
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# logger.debug(processed)
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month = re.search(r"\d{2}$", processed).group()
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processed = rreplace(processed, month, "")
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processed = processed.replace("--", "")
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logger.debug(processed)
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# logger.debug(processed)
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year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
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year = f"20{year}"
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logger.debug(processed)
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# logger.debug(processed)
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final_en_name = f"PBS{year}{month}{day}-{plate_num}"
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return final_en_name
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@@ -2881,7 +2835,7 @@ class BacterialCultureSample(BasicSample):
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sample['organism'] = self.organism
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try:
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sample['concentration'] = f"{float(self.concentration):.2f}"
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except TypeError:
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except (TypeError, ValueError):
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sample['concentration'] = 0.0
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if self.control is not None:
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sample['colour'] = [0, 128, 0]
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