New table view.
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lwark
@@ -54,7 +54,7 @@ class ClientSubmission(BaseClass, LogMixin):
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_submission_category = Column(
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String(64)) #: ["Research", "Diagnostic", "Surveillance", "Validation"], else defaults to submission_type_name
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sample_count = Column(INTEGER) #: Number of samples in the submission
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comment = Column(JSON)
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runs = relationship("BasicSubmission", back_populates="client_submission") #: many-to-one relationship
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contact = relationship("Contact", back_populates="submissions") #: client org
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@@ -92,6 +92,192 @@ class ClientSubmission(BaseClass, LogMixin):
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except AttributeError:
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self._submission_category = "NA"
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@classmethod
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def recruit_parser(cls):
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pass
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@classmethod
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@setup_lookup
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def query(cls,
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submissiontype: str | SubmissionType | None = None,
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submission_type_name: str | None = None,
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id: int | str | None = None,
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submitter_plate_num: str | None = None,
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start_date: date | datetime | str | int | None = None,
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end_date: date | datetime | str | int | None = None,
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chronologic: bool = False,
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limit: int = 0,
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page: int = 1,
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page_size: None | int = 250,
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**kwargs
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) -> BasicSubmission | List[BasicSubmission]:
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"""
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Lookup submissions based on a number of parameters. Overrides parent.
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Args:
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submission_type (str | models.SubmissionType | None, optional): Submission type of interest. Defaults to None.
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id (int | str | None, optional): Submission id in the database (limits results to 1). Defaults to None.
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rsl_plate_num (str | None, optional): Submission name in the database (limits results to 1). Defaults to None.
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start_date (date | str | int | None, optional): Beginning date to search by. Defaults to None.
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end_date (date | str | int | None, optional): Ending date to search by. Defaults to None.
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reagent (models.Reagent | str | None, optional): A reagent used in the submission. Defaults to None.
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chronologic (bool, optional): Return results in chronologic order. Defaults to False.
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limit (int, optional): Maximum number of results to return. Defaults to 0.
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Returns:
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models.BasicSubmission | List[models.BasicSubmission]: Submission(s) of interest
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"""
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# from ... import SubmissionReagentAssociation
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# NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters
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query: Query = cls.__database_session__.query(cls)
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if start_date is not None and end_date is None:
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logger.warning(f"Start date with no end date, using today.")
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end_date = date.today()
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if end_date is not None and start_date is None:
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# NOTE: this query returns a tuple of (object, datetime), need to get only datetime.
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start_date = cls.__database_session__.query(cls, func.min(cls.submitted_date)).first()[1]
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logger.warning(f"End date with no start date, using first submission date: {start_date}")
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if start_date is not None:
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start_date = cls.rectify_query_date(start_date)
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end_date = cls.rectify_query_date(end_date, eod=True)
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logger.debug(f"Start date: {start_date}, end date: {end_date}")
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query = query.filter(cls.submitted_date.between(start_date, end_date))
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# NOTE: by rsl number (returns only a single value)
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match submitter_plate_num:
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case str():
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query = query.filter(cls.submitter_plate_num == submitter_plate_num)
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limit = 1
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case _:
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pass
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match submission_type_name:
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case str():
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query = query.filter(cls.submission_type_name == submission_type_name)
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case _:
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pass
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# NOTE: by id (returns only a single value)
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match id:
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case int():
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query = query.filter(cls.id == id)
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limit = 1
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case str():
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query = query.filter(cls.id == int(id))
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limit = 1
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case _:
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pass
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# query = query.order_by(cls.submitted_date.desc())
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# NOTE: Split query results into pages of size {page_size}
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if page_size > 0:
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query = query.limit(page_size)
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page = page - 1
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if page is not None:
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query = query.offset(page * page_size)
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return cls.execute_query(query=query, model=cls, limit=limit, **kwargs)
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@classmethod
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def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0,
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chronologic: bool = True, page: int = 1, page_size: int = 250) -> pd.DataFrame:
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"""
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Convert all submissions to dataframe
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Args:
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page_size (int, optional): Number of items to include in query result. Defaults to 250.
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page (int, optional): Limits the number of submissions to a page size. Defaults to 1.
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chronologic (bool, optional): Sort submissions in chronologic order. Defaults to True.
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submission_type (str | None, optional): Filter by SubmissionType. Defaults to None.
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limit (int, optional): Maximum number of results to return. Defaults to 0.
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Returns:
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pd.DataFrame: Pandas Dataframe of all relevant submissions
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"""
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# NOTE: use lookup function to create list of dicts
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subs = [item.to_dict() for item in
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cls.query(submissiontype=submission_type, limit=limit, chronologic=chronologic, page=page,
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page_size=page_size)]
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df = pd.DataFrame.from_records(subs)
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# NOTE: Exclude sub information
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exclude = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
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'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
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'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
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'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact',
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'tips', 'gel_image_path', 'custom']
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# NOTE: dataframe equals dataframe of all columns not in exclude
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df = df.loc[:, ~df.columns.isin(exclude)]
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if chronologic:
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try:
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df.sort_values(by="id", axis=0, inplace=True, ascending=False)
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except KeyError:
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logger.error("No column named 'id'")
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# NOTE: Human friendly column labels
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df.columns = [item.replace("_", " ").title() for item in df.columns]
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return df
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def to_dict(self, full_data: bool = False, backup: bool = False, report: bool = False) -> dict:
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"""
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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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Returns:
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dict: dictionary used in submissions summary and details
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"""
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# NOTE: get lab from nested organization object
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try:
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sub_lab = self.submitting_lab.name
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except AttributeError:
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sub_lab = None
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try:
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sub_lab = sub_lab.replace("_", " ").title()
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except AttributeError:
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pass
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# NOTE: get extraction kit name from nested kit object
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output = {
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"id": self.id,
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"submission_type": self.submission_type_name,
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"submitter_plate_number": self.submitter_plate_num,
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"submitted_date": self.submitted_date.strftime("%Y-%m-%d"),
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"submitting_lab": sub_lab,
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"sample_count": self.sample_count,
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}
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if report:
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return output
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if full_data:
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# dicto, _ = self.extraction_kit.construct_xl_map_for_use(self.submission_type)
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# samples = self.generate_associations(name="submission_sample_associations")
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samples = None
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runs = [item.to_dict() for item in self.runs]
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# custom = self.custom
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else:
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samples = None
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custom = None
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runs = None
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try:
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comments = self.comment
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except Exception as e:
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logger.error(f"Error setting comment: {self.comment}, {e}")
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comments = None
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try:
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contact = self.contact.name
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except AttributeError as e:
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try:
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contact = f"Defaulted to: {self.submitting_lab.contacts[0].name}"
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except (AttributeError, IndexError):
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contact = "NA"
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try:
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contact_phone = self.contact.phone
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except AttributeError:
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contact_phone = "NA"
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output["submission_category"] = self.submission_category
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output["samples"] = samples
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output["comment"] = comments
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output["contact"] = contact
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output["contact_phone"] = contact_phone
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# output["custom"] = custom
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output["runs"] = runs
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return output
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class BasicSubmission(BaseClass, LogMixin):
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"""
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