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Pre-cleanup

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This commit is contained in:
Landon Wark
2023-11-01 08:59:58 -05:00
parent f3a7d75c6a
commit 22a23b7838
18 changed files with 665 additions and 636 deletions
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18
src/submissions/backend/db/models/submissions.py
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@@ -47,6 +47,7 @@ class BasicSubmission(Base):
reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
extraction_info = Column(JSON) #: unstructured output from the extraction table logger.
pcr_info = Column(JSON) #: unstructured output from pcr table logger or user(Artic)
run_cost = Column(FLOAT(2)) #: total cost of running the plate. Set from constant and mutable kit costs at time of creation.
uploaded_by = Column(String(32)) #: user name of person who submitted the submission to the database.
comment = Column(JSON)
@@ -211,12 +212,12 @@ class BasicSubmission(Base):
Calculate the number of columns in this submission
Returns:
int: largest column number
int: Number of unique columns.
"""
logger.debug(f"Here's the samples: {self.samples}")
columns = [assoc.column for assoc in self.submission_sample_associations]
columns = set([assoc.column for assoc in self.submission_sample_associations])
logger.debug(f"Here are the columns for {self.rsl_plate_num}: {columns}")
return max(columns)
return len(columns)
def hitpick_plate(self, plate_number:int|None=None) -> list:
"""
@@ -281,7 +282,7 @@ class BasicSubmission(Base):
Returns:
dict: Updated sample dictionary
"""
logger.debug(f"Called {cls.__name__} sample parser")
# logger.debug(f"Called {cls.__name__} sample parser")
return input_dict
@classmethod
@@ -461,7 +462,7 @@ class Wastewater(BasicSubmission):
"""
derivative submission type from BasicSubmission
"""
pcr_info = Column(JSON)
# pcr_info = Column(JSON)
ext_technician = Column(String(64))
pcr_technician = Column(String(64))
__mapper_args__ = {"polymorphic_identity": "Wastewater", "polymorphic_load": "inline"}
@@ -570,13 +571,16 @@ class Wastewater(BasicSubmission):
@classmethod
def get_regex(cls):
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?)"
# return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?)"
# return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?([^_|\D]|$)R?\d?)?)"
return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789]|$)R?\d?)?)"
class WastewaterArtic(BasicSubmission):
"""
derivative submission type for artic wastewater
"""
__mapper_args__ = {"polymorphic_identity": "Wastewater Artic", "polymorphic_load": "inline"}
artic_technician = Column(String(64))
def calculate_base_cost(self):
"""
@@ -752,7 +756,7 @@ class BasicSample(Base):
@classmethod
def parse_sample(cls, input_dict:dict) -> dict:
logger.debug(f"Called {cls.__name__} sample parser")
# logger.debug(f"Called {cls.__name__} sample parser")
return input_dict
class WastewaterSample(BasicSample):