Writer and manager updates.
This commit is contained in:
lwark
@@ -516,44 +516,6 @@ class PydRun(PydBaseClass, extra='allow'):
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value = dict(value=value, missing=True)
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return value
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# @field_validator("tips", mode="before")
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# @classmethod
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# def expand_tips(cls, value):
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# if isinstance(value, dict):
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# value = value['value']
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# if isinstance(value, Generator):
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# return [PydTips(**tips) for tips in value]
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# if not value:
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# return []
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# return value
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#
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# @field_validator('equipment', mode='before')
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# @classmethod
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# def convert_equipment_dict(cls, value):
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# if isinstance(value, dict):
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# return value['value']
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# if isinstance(value, Generator):
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# return [PydEquipment(**equipment) for equipment in value]
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# if not value:
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# return []
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# return value
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# @field_validator('comment', mode='before')
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# @classmethod
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# def create_comment(cls, value):
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# if value is None:
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# return ""
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# return value
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#
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# @field_validator("submitter_plate_id")
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# @classmethod
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# def enforce_with_uuid(cls, value):
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# if value['value'] in [None, "None"]:
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# return dict(value=uuid.uuid4().hex.upper(), missing=True)
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# else:
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# value['value'] = value['value'].strip()
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# return value
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@field_validator("run_cost")
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@classmethod
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def rescue_run_cost(cls, value):
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@@ -635,36 +597,6 @@ class PydRun(PydBaseClass, extra='allow'):
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value['value'] = output.replace(tzinfo=timezone)
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return value
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# @field_validator("clientlab", mode="before")
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# @classmethod
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# def rescue_submitting_lab(cls, value):
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# if value is None:
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# return dict(value=None, missing=True)
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# return value
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#
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# @field_validator("clientlab")
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# @classmethod
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# def lookup_submitting_lab(cls, value):
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# if isinstance(value['value'], str):
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# try:
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# value['value'] = ClientLab.query(name=value['value']).name
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# except AttributeError:
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# value['value'] = None
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# if value['value'] is None:
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# value['missing'] = True
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# if "pytest" in sys.modules:
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# value['value'] = "Nosocomial"
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# return value
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# from frontend.widgets.pop_ups import ObjectSelector
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# dlg = ObjectSelector(title="Missing Submitting Lab",
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# message="We need a submitting lab. Please select from the list.",
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# obj_type=ClientLab)
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# if dlg.exec():
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# value['value'] = dlg.parse_form()
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# else:
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# value['value'] = None
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# return value
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@field_validator("rsl_plate_number", mode='before')
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@classmethod
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def rescue_rsl_number(cls, value):
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@@ -686,26 +618,8 @@ class PydRun(PydBaseClass, extra='allow'):
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# try:
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output = RSLNamer(filename=sub_type.filepath.__str__(), submission_type=sub_type.submissiontype,
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data=values.data).parsed_name
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return dict(value=output, missing=True)
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# @field_validator("technician", mode="before")
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# @classmethod
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# def rescue_tech(cls, value):
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# if value is None:
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# return dict(value=None, missing=True)
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# return value
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#
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# @field_validator("technician")
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# @classmethod
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# def enforce_tech(cls, value):
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# if check_not_nan(value['value']):
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# value['value'] = re.sub(r"\: \d", "", value['value'])
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# return value
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# else:
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# return dict(value=convert_nans_to_nones(value['value']), missing=True)
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@field_validator("sample_count", mode='before')
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@classmethod
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def rescue_sample_count(cls, value):
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@@ -713,55 +627,6 @@ class PydRun(PydBaseClass, extra='allow'):
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return dict(value=None, missing=True)
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return value
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# @field_validator("kittype", mode='before')
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# @classmethod
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# def rescue_kit(cls, value):
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# if check_not_nan(value):
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# if isinstance(value, str):
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# return dict(value=value, missing=False)
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# elif isinstance(value, dict):
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# return value
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# else:
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# raise ValueError(f"No extraction kittype found.")
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# if value is None:
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# # NOTE: Kit selection is done in the clientsubmissionparser, so should not be necessary here.
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# return dict(value=None, missing=True)
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# return value
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#
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# @field_validator("submissiontype", mode='before')
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# @classmethod
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# def make_submission_type(cls, value, values):
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# if not isinstance(value, dict):
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# value = dict(value=value)
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# if check_not_nan(value['value']):
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# value = value['value'].title()
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# return dict(value=value, missing=False)
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# else:
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# return dict(value=RSLNamer.retrieve_submission_type(filename=values.data['filepath']).title(), missing=True)
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#
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# @field_validator("submission_category", mode="before")
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# @classmethod
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# def create_category(cls, value):
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# if not isinstance(value, dict):
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# return dict(value=value, missing=True)
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# return value
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#
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# @field_validator("submission_category")
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# @classmethod
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# def rescue_category(cls, value, values):
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# if isinstance(value['value'], str):
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# value['value'] = value['value'].title()
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# if value['value'] not in ["Research", "Diagnostic", "Surveillance", "Validation"]:
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# value['value'] = values.data['proceduretype']['value']
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# return value
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# @field_validator("reagent", mode="before")
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# @classmethod
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# def expand_reagents(cls, value):
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# if isinstance(value, Generator):
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# return [PydReagent(**reagent) for reagent in value]
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# return value
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@field_validator("sample", mode="before")
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@classmethod
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def expand_samples(cls, value):
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@@ -769,77 +634,9 @@ class PydRun(PydBaseClass, extra='allow'):
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return [PydSample(**sample) for sample in value]
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return value
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# @field_validator("sample")
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# @classmethod
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# def assign_ids(cls, value):
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# starting_id = ClientSubmissionSampleAssociation.autoincrement_id()
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# for iii, sample in enumerate(value, start=starting_id):
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# # NOTE: Why is this a list? Answer: to zip with the lists of rows and columns in case of multiple of the same sample.
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# sample.assoc_id = [iii]
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# return value
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# @field_validator("cost_centre", mode="before")
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# @classmethod
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# def rescue_cost_centre(cls, value):
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# match value:
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# case dict():
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# return value
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# case _:
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# return dict(value=value, missing=True)
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#
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# @field_validator("cost_centre")
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# @classmethod
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# def get_cost_centre(cls, value, values):
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# match value['value']:
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# case None:
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# from backend.db.models import Organization
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# org = Organization.query(name=values.data['clientlab']['value'])
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# try:
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# return dict(value=org.cost_centre, missing=True)
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# except AttributeError:
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# return dict(value="xxx", missing=True)
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# case _:
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# return value
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#
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# @field_validator("contact")
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# @classmethod
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# def get_contact_from_org(cls, value, values):
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# # logger.debug(f"Value coming in: {value}")
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# match value:
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# case dict():
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# if isinstance(value['value'], tuple):
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# value['value'] = value['value'][0]
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# case tuple():
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# value = dict(value=value[0], missing=False)
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# case _:
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# value = dict(value=value, missing=False)
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# # logger.debug(f"Value after match: {value}")
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# check = Contact.query(name=value['value'])
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# # logger.debug(f"Check came back with {check}")
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# if not isinstance(check, Contact):
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# org = values.data['clientlab']['value']
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# # logger.debug(f"Checking organization: {org}")
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# if isinstance(org, str):
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# org = ClientLab.query(name=values.data['clientlab']['value'], limit=1)
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# if isinstance(org, ClientLab):
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# contact = org.contact[0].name
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# else:
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# logger.warning(f"All attempts at defaulting Contact failed, returning: {value}")
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# return value
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# if isinstance(contact, tuple):
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# contact = contact[0]
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# value = dict(value=f"Defaulted to: {contact}", missing=False)
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# # logger.debug(f"Value after query: {value}")
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# return value
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# else:
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# # logger.debug(f"Value after bypass check: {value}")
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# return value
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def __init__(self, run_custom: bool = False, **data):
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super().__init__(**data)
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# NOTE: this could also be done with default_factory
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# self.submission_object = Run.find_polymorphic_subclass(
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# polymorphic_identity=self.submission_type['value'])
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submission_type = self.clientsubmission.submissiontype
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# logger.debug(submission_type)
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self.namer = RSLNamer(self.rsl_plate_number['value'], submission_type=submission_type)
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@@ -1504,6 +1301,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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name: dict = Field(default=dict(value="NA", missing=True), validate_default=True)
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technician: dict = Field(default=dict(value="NA", missing=True))
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repeat: bool = Field(default=False)
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repeat_of: str | None = Field(default=None)
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kittype: dict = Field(default=dict(value="NA", missing=True))
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possible_kits: list | None = Field(default=[], validate_default=True)
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plate_map: str | None = Field(default=None)
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@@ -1516,6 +1314,8 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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@field_validator("name", "technician", "kittype", mode="before")
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@classmethod
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def convert_to_dict(cls, value):
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if not value:
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value = "NA"
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if isinstance(value, str):
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value = dict(value=value, missing=False)
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return value
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@@ -1597,6 +1397,13 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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value = Run.query(name=value)
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return value
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@field_validator("repeat_of")
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@classmethod
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def drop_empty_string(cls, value):
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if value == "":
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value = None
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return value
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def update_kittype_reagentroles(self, kittype: str | KitType):
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if kittype == self.__class__.model_fields['kittype'].default['value']:
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return
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@@ -1687,14 +1494,21 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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reg = reagent.to_sql()
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reg.save()
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def to_sql(self):
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def to_sql(self, new: bool=False):
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from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
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# results = []
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# for result in self.results:
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# result, _ = result.to_sql()
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sql = super().to_sql()
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# logger.debug(f"Initial PYD: {pformat(self.__dict__)}")
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if new:
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sql = Procedure()
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else:
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sql = super().to_sql()
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logger.debug(f"Initial PYD: {pformat(self.__dict__)}")
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# sql.results = [result.to_sql() for result in self.results]
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sql.repeat = self.repeat
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if sql.repeat:
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regex = re.compile(r".*\dR\d$")
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repeats = [item for item in self.run.procedure if self.repeat_of in item.name and bool(regex.match(item.name))]
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sql.name = f"{self.repeat_of}R{str(len(repeats)+1)}"
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sql.repeat_of = self.repeat_of
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sql.started_date = datetime.now()
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if self.run:
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sql.run = self.run
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if self.proceduretype:
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@@ -1710,13 +1524,16 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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for reagent in self.reagent:
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if isinstance(reagent, dict):
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reagent = PydReagent(**reagent)
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logger.debug(reagent)
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# logger.debug(reagent)
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reagentrole = reagent.reagentrole
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reagent = reagent.to_sql()
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logger.debug(reagentrole)
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# logger.debug(reagentrole)
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if reagent not in sql.reagent:
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# NOTE: Remove any previous association for this role.
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removable = ProcedureReagentAssociation.query(procedure=sql, reagentrole=reagentrole)
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if sql.id:
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removable = ProcedureReagentAssociation.query(procedure=sql, reagentrole=reagentrole)
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else:
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removable = []
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logger.debug(f"Removable: {removable}")
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if removable:
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if isinstance(removable, list):
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@@ -1724,7 +1541,7 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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r.delete()
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else:
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removable.delete()
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logger.debug(f"Adding {reagent} to {sql}")
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# logger.debug(f"Adding {reagent} to {sql}")
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reagent_assoc = ProcedureReagentAssociation(reagent=reagent, procedure=sql, reagentrole=reagentrole)
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try:
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start_index = max([item.id for item in ProcedureSampleAssociation.query()]) + 1
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@@ -1732,9 +1549,9 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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start_index = 1
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relevant_samples = [sample for sample in self.sample if
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not sample.sample_id.startswith("blank_") and not sample.sample_id == ""]
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logger.debug(f"start index: {start_index}")
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# logger.debug(f"start index: {start_index}")
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assoc_id_range = range(start_index, start_index + len(relevant_samples) + 1)
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logger.debug(f"Association id range: {assoc_id_range}")
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# logger.debug(f"Association id range: {assoc_id_range}")
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for iii, sample in enumerate(relevant_samples):
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sample_sql = sample.to_sql()
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if sql.run:
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@@ -1751,11 +1568,6 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
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kittype = KitType.query(name=self.kittype['value'], limit=1)
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if kittype:
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sql.kittype = kittype
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# logger.debug(self.reagent)
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# for reagent in self.reagent:
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# reagent = reagent.to_sql()
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# if reagent not in sql.reagent:
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# reagent_assoc = ProcedureReagentAssociation(reagent=reagent, procedure=sql)
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for equipment in self.equipment:
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equip = Equipment.query(name=equipment.name)
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if equip not in sql.equipment:
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@@ -1859,7 +1671,7 @@ class PydClientSubmission(PydBaseClass):
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if not value['value'] in ["Research", "Diagnostic", "Surveillance", "Validation"]:
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try:
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value['value'] = values.data['submissiontype']['value']
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except AttributeError:
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except (AttributeError, KeyError):
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value['value'] = "NA"
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return value
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@@ -1938,7 +1750,7 @@ class PydClientSubmission(PydBaseClass):
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class PydResults(PydBaseClass, arbitrary_types_allowed=True):
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results: dict = Field(default={})
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results_type: str = Field(default="NA")
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result_type: str = Field(default="NA")
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img: None | bytes = Field(default=None)
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parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
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date_analyzed: datetime | None = Field(default=None)
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@@ -1956,7 +1768,7 @@ class PydResults(PydBaseClass, arbitrary_types_allowed=True):
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return value
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def to_sql(self):
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sql, _ = Results.query_or_create(results_type=self.results_type, result=self.results)
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sql, _ = Results.query_or_create(result_type=self.result_type, result=self.results)
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try:
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check = sql.image
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except FileNotFoundError:
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