New table view.
This commit is contained in:
lwark
@@ -221,10 +221,10 @@ class BaseClass(Base):
|
||||
Returns:
|
||||
Any | List[Any]: Single result if limit = 1 or List if other.
|
||||
"""
|
||||
logger.debug(f"Kwargs: {kwargs}")
|
||||
# logger.debug(f"Kwargs: {kwargs}")
|
||||
if model is None:
|
||||
model = cls
|
||||
logger.debug(f"Model: {model}")
|
||||
# logger.debug(f"Model: {model}")
|
||||
if query is None:
|
||||
query: Query = cls.__database_session__.query(model)
|
||||
singles = model.get_default_info('singles')
|
||||
@@ -516,7 +516,7 @@ from .controls import *
|
||||
from .organizations import *
|
||||
from .kits import *
|
||||
from .submissions import *
|
||||
from .audit import *
|
||||
from .audit import AuditLog
|
||||
|
||||
# NOTE: Add a creator to the submission for reagent association. Assigned here due to circular import constraints.
|
||||
# https://docs.sqlalchemy.org/en/20/orm/extensions/associationproxy.html#sqlalchemy.ext.associationproxy.association_proxy.params.creator
|
||||
|
||||
@@ -1289,6 +1289,7 @@ class SubmissionType(BaseClass):
|
||||
query: Query = cls.__database_session__.query(cls)
|
||||
match name:
|
||||
case str():
|
||||
logger.debug(f"querying with {name}")
|
||||
query = query.filter(cls.name == name)
|
||||
limit = 1
|
||||
case _:
|
||||
|
||||
@@ -54,7 +54,7 @@ class ClientSubmission(BaseClass, LogMixin):
|
||||
_submission_category = Column(
|
||||
String(64)) #: ["Research", "Diagnostic", "Surveillance", "Validation"], else defaults to submission_type_name
|
||||
sample_count = Column(INTEGER) #: Number of samples in the submission
|
||||
|
||||
comment = Column(JSON)
|
||||
runs = relationship("BasicSubmission", back_populates="client_submission") #: many-to-one relationship
|
||||
|
||||
contact = relationship("Contact", back_populates="submissions") #: client org
|
||||
@@ -92,6 +92,192 @@ class ClientSubmission(BaseClass, LogMixin):
|
||||
except AttributeError:
|
||||
self._submission_category = "NA"
|
||||
|
||||
@classmethod
|
||||
def recruit_parser(cls):
|
||||
pass
|
||||
|
||||
@classmethod
|
||||
@setup_lookup
|
||||
def query(cls,
|
||||
submissiontype: str | SubmissionType | None = None,
|
||||
submission_type_name: str | None = None,
|
||||
id: int | str | None = None,
|
||||
submitter_plate_num: str | None = None,
|
||||
start_date: date | datetime | str | int | None = None,
|
||||
end_date: date | datetime | str | int | None = None,
|
||||
chronologic: bool = False,
|
||||
limit: int = 0,
|
||||
page: int = 1,
|
||||
page_size: None | int = 250,
|
||||
**kwargs
|
||||
) -> BasicSubmission | List[BasicSubmission]:
|
||||
"""
|
||||
Lookup submissions based on a number of parameters. Overrides parent.
|
||||
|
||||
Args:
|
||||
submission_type (str | models.SubmissionType | None, optional): Submission type of interest. Defaults to None.
|
||||
id (int | str | None, optional): Submission id in the database (limits results to 1). Defaults to None.
|
||||
rsl_plate_num (str | None, optional): Submission name in the database (limits results to 1). Defaults to None.
|
||||
start_date (date | str | int | None, optional): Beginning date to search by. Defaults to None.
|
||||
end_date (date | str | int | None, optional): Ending date to search by. Defaults to None.
|
||||
reagent (models.Reagent | str | None, optional): A reagent used in the submission. Defaults to None.
|
||||
chronologic (bool, optional): Return results in chronologic order. Defaults to False.
|
||||
limit (int, optional): Maximum number of results to return. Defaults to 0.
|
||||
|
||||
Returns:
|
||||
models.BasicSubmission | List[models.BasicSubmission]: Submission(s) of interest
|
||||
"""
|
||||
# from ... import SubmissionReagentAssociation
|
||||
# NOTE: if you go back to using 'model' change the appropriate cls to model in the query filters
|
||||
query: Query = cls.__database_session__.query(cls)
|
||||
if start_date is not None and end_date is None:
|
||||
logger.warning(f"Start date with no end date, using today.")
|
||||
end_date = date.today()
|
||||
if end_date is not None and start_date is None:
|
||||
# NOTE: this query returns a tuple of (object, datetime), need to get only datetime.
|
||||
start_date = cls.__database_session__.query(cls, func.min(cls.submitted_date)).first()[1]
|
||||
logger.warning(f"End date with no start date, using first submission date: {start_date}")
|
||||
if start_date is not None:
|
||||
start_date = cls.rectify_query_date(start_date)
|
||||
end_date = cls.rectify_query_date(end_date, eod=True)
|
||||
logger.debug(f"Start date: {start_date}, end date: {end_date}")
|
||||
query = query.filter(cls.submitted_date.between(start_date, end_date))
|
||||
# NOTE: by rsl number (returns only a single value)
|
||||
match submitter_plate_num:
|
||||
case str():
|
||||
query = query.filter(cls.submitter_plate_num == submitter_plate_num)
|
||||
limit = 1
|
||||
case _:
|
||||
pass
|
||||
match submission_type_name:
|
||||
case str():
|
||||
query = query.filter(cls.submission_type_name == submission_type_name)
|
||||
case _:
|
||||
pass
|
||||
# NOTE: by id (returns only a single value)
|
||||
match id:
|
||||
case int():
|
||||
query = query.filter(cls.id == id)
|
||||
limit = 1
|
||||
case str():
|
||||
query = query.filter(cls.id == int(id))
|
||||
limit = 1
|
||||
case _:
|
||||
pass
|
||||
# query = query.order_by(cls.submitted_date.desc())
|
||||
# NOTE: Split query results into pages of size {page_size}
|
||||
if page_size > 0:
|
||||
query = query.limit(page_size)
|
||||
page = page - 1
|
||||
if page is not None:
|
||||
query = query.offset(page * page_size)
|
||||
return cls.execute_query(query=query, model=cls, limit=limit, **kwargs)
|
||||
|
||||
@classmethod
|
||||
def submissions_to_df(cls, submission_type: str | None = None, limit: int = 0,
|
||||
chronologic: bool = True, page: int = 1, page_size: int = 250) -> pd.DataFrame:
|
||||
"""
|
||||
Convert all submissions to dataframe
|
||||
|
||||
Args:
|
||||
page_size (int, optional): Number of items to include in query result. Defaults to 250.
|
||||
page (int, optional): Limits the number of submissions to a page size. Defaults to 1.
|
||||
chronologic (bool, optional): Sort submissions in chronologic order. Defaults to True.
|
||||
submission_type (str | None, optional): Filter by SubmissionType. Defaults to None.
|
||||
limit (int, optional): Maximum number of results to return. Defaults to 0.
|
||||
|
||||
Returns:
|
||||
pd.DataFrame: Pandas Dataframe of all relevant submissions
|
||||
"""
|
||||
# NOTE: use lookup function to create list of dicts
|
||||
subs = [item.to_dict() for item in
|
||||
cls.query(submissiontype=submission_type, limit=limit, chronologic=chronologic, page=page,
|
||||
page_size=page_size)]
|
||||
df = pd.DataFrame.from_records(subs)
|
||||
# NOTE: Exclude sub information
|
||||
exclude = ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents',
|
||||
'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'gel_controls',
|
||||
'source_plates', 'pcr_technician', 'ext_technician', 'artic_technician', 'cost_centre',
|
||||
'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact',
|
||||
'tips', 'gel_image_path', 'custom']
|
||||
# NOTE: dataframe equals dataframe of all columns not in exclude
|
||||
df = df.loc[:, ~df.columns.isin(exclude)]
|
||||
if chronologic:
|
||||
try:
|
||||
df.sort_values(by="id", axis=0, inplace=True, ascending=False)
|
||||
except KeyError:
|
||||
logger.error("No column named 'id'")
|
||||
# NOTE: Human friendly column labels
|
||||
df.columns = [item.replace("_", " ").title() for item in df.columns]
|
||||
return df
|
||||
|
||||
def to_dict(self, full_data: bool = False, backup: bool = False, report: bool = False) -> dict:
|
||||
"""
|
||||
Constructs dictionary used in submissions summary
|
||||
|
||||
Args:
|
||||
expand (bool, optional): indicates if generators to be expanded. Defaults to False.
|
||||
report (bool, optional): indicates if to be used for a report. Defaults to False.
|
||||
full_data (bool, optional): indicates if sample dicts to be constructed. Defaults to False.
|
||||
backup (bool, optional): passed to adjust_to_dict_samples. Defaults to False.
|
||||
|
||||
Returns:
|
||||
dict: dictionary used in submissions summary and details
|
||||
"""
|
||||
# NOTE: get lab from nested organization object
|
||||
try:
|
||||
sub_lab = self.submitting_lab.name
|
||||
except AttributeError:
|
||||
sub_lab = None
|
||||
try:
|
||||
sub_lab = sub_lab.replace("_", " ").title()
|
||||
except AttributeError:
|
||||
pass
|
||||
# NOTE: get extraction kit name from nested kit object
|
||||
output = {
|
||||
"id": self.id,
|
||||
"submission_type": self.submission_type_name,
|
||||
"submitter_plate_number": self.submitter_plate_num,
|
||||
"submitted_date": self.submitted_date.strftime("%Y-%m-%d"),
|
||||
"submitting_lab": sub_lab,
|
||||
"sample_count": self.sample_count,
|
||||
}
|
||||
if report:
|
||||
return output
|
||||
if full_data:
|
||||
# dicto, _ = self.extraction_kit.construct_xl_map_for_use(self.submission_type)
|
||||
# samples = self.generate_associations(name="submission_sample_associations")
|
||||
samples = None
|
||||
runs = [item.to_dict() for item in self.runs]
|
||||
# custom = self.custom
|
||||
else:
|
||||
samples = None
|
||||
custom = None
|
||||
runs = None
|
||||
try:
|
||||
comments = self.comment
|
||||
except Exception as e:
|
||||
logger.error(f"Error setting comment: {self.comment}, {e}")
|
||||
comments = None
|
||||
try:
|
||||
contact = self.contact.name
|
||||
except AttributeError as e:
|
||||
try:
|
||||
contact = f"Defaulted to: {self.submitting_lab.contacts[0].name}"
|
||||
except (AttributeError, IndexError):
|
||||
contact = "NA"
|
||||
try:
|
||||
contact_phone = self.contact.phone
|
||||
except AttributeError:
|
||||
contact_phone = "NA"
|
||||
output["submission_category"] = self.submission_category
|
||||
output["samples"] = samples
|
||||
output["comment"] = comments
|
||||
output["contact"] = contact
|
||||
output["contact_phone"] = contact_phone
|
||||
# output["custom"] = custom
|
||||
output["runs"] = runs
|
||||
return output
|
||||
|
||||
class BasicSubmission(BaseClass, LogMixin):
|
||||
"""
|
||||
|
||||
Reference in New Issue
Block a user