Removed logger.debugs for proven functions.
This commit is contained in:
lwark
@@ -17,7 +17,6 @@ from io import BytesIO
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logger = logging.getLogger(f'submissions.{__name__}')
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# logger.debug("Table for ReagentType/Reagent relations")
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reagentroles_reagents = Table(
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"_reagentroles_reagents",
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Base.metadata,
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@@ -26,7 +25,6 @@ reagentroles_reagents = Table(
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extend_existing=True
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)
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# logger.debug("Table for EquipmentRole/Equipment relations")
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equipmentroles_equipment = Table(
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"_equipmentroles_equipment",
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Base.metadata,
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@@ -35,7 +33,6 @@ equipmentroles_equipment = Table(
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extend_existing=True
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)
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# logger.debug("Table for Equipment/Process relations")
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equipment_processes = Table(
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"_equipment_processes",
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Base.metadata,
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@@ -44,7 +41,6 @@ equipment_processes = Table(
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extend_existing=True
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)
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# logger.debug("Table for EquipmentRole/Process relations")
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equipmentroles_processes = Table(
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"_equipmentroles_processes",
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Base.metadata,
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@@ -53,7 +49,6 @@ equipmentroles_processes = Table(
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extend_existing=True
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)
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# logger.debug("Table for SubmissionType/Process relations")
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submissiontypes_processes = Table(
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"_submissiontypes_processes",
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Base.metadata,
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@@ -62,7 +57,6 @@ submissiontypes_processes = Table(
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extend_existing=True
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)
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# logger.debug("Table for KitType/Process relations")
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kittypes_processes = Table(
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"_kittypes_processes",
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Base.metadata,
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@@ -71,7 +65,6 @@ kittypes_processes = Table(
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extend_existing=True
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)
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# logger.debug("Table for TipRole/Tips relations")
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tiproles_tips = Table(
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"_tiproles_tips",
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Base.metadata,
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@@ -80,7 +73,6 @@ tiproles_tips = Table(
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extend_existing=True
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)
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# logger.debug("Table for Process/TipRole relations")
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process_tiprole = Table(
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"_process_tiprole",
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Base.metadata,
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@@ -89,7 +81,6 @@ process_tiprole = Table(
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extend_existing=True
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)
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# logger.debug("Table for Equipment/Tips relations")
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equipment_tips = Table(
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"_equipment_tips",
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Base.metadata,
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@@ -116,7 +107,7 @@ class KitType(BaseClass):
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cascade="all, delete-orphan",
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)
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# creator function: https://stackoverflow.com/questions/11091491/keyerror-when-adding-objects-to-sqlalchemy-association-object/11116291#11116291
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# NOTE: creator function: https://stackoverflow.com/questions/11091491/keyerror-when-adding-objects-to-sqlalchemy-association-object/11116291#11116291
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reagent_roles = association_proxy("kit_reagentrole_associations", "reagent_role",
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creator=lambda RT: KitTypeReagentRoleAssociation(
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reagent_role=RT)) #: Association proxy to KitTypeReagentRoleAssociation
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@@ -152,18 +143,14 @@ class KitType(BaseClass):
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"""
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match submission_type:
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case SubmissionType():
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# logger.debug(f"Getting reagents by SubmissionType {submission_type}")
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relevant_associations = [item for item in self.kit_reagentrole_associations if
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item.submission_type == submission_type]
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case str():
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# logger.debug(f"Getting reagents by str {submission_type}")
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relevant_associations = [item for item in self.kit_reagentrole_associations if
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item.submission_type.name == submission_type]
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case _:
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# logger.debug(f"Getting reagents")
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relevant_associations = [item for item in self.kit_reagentrole_associations]
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if required:
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# logger.debug(f"Filtering by required.")
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return (item.reagent_role for item in relevant_associations if item.required == 1)
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else:
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return (item.reagent_role for item in relevant_associations)
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@@ -181,18 +168,14 @@ class KitType(BaseClass):
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# NOTE: Account for submission_type variable type.
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match submission_type:
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case str():
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# logger.debug(f"Constructing xl map with str {submission_type}")
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assocs = [item for item in self.kit_reagentrole_associations if
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item.submission_type.name == submission_type]
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case SubmissionType():
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# logger.debug(f"Constructing xl map with SubmissionType {submission_type}")
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assocs = [item for item in self.kit_reagentrole_associations if item.submission_type == submission_type]
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case _:
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raise ValueError(f"Wrong variable type: {type(submission_type)} used!")
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# logger.debug("Get all KitTypeReagentTypeAssociation for SubmissionType")
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for assoc in assocs:
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try:
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# logger.debug(f"Yielding: {assoc.reagent_role.name}, {assoc.uses}")
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yield assoc.reagent_role.name, assoc.uses
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except TypeError:
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continue
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@@ -220,27 +203,22 @@ class KitType(BaseClass):
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query: Query = cls.__database_session__.query(cls)
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match used_for:
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case str():
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# logger.debug(f"Looking up kit type by used_for str: {used_for}")
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query = query.filter(cls.used_for.any(name=used_for))
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case SubmissionType():
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# logger.debug(f"Looking up kit type by used_for SubmissionType: {used_for}")
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query = query.filter(cls.used_for.contains(used_for))
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case _:
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pass
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match name:
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case str():
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# logger.debug(f"Looking up kit type by name str: {name}")
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query = query.filter(cls.name == name)
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limit = 1
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case _:
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pass
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match id:
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case int():
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# logger.debug(f"Looking up kit type by id int: {id}")
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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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# logger.debug(f"Looking up kit type by id str: {id}")
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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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@@ -262,10 +240,7 @@ class KitType(BaseClass):
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dict: Dictionary containing relevant info for SubmissionType construction
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"""
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base_dict = dict(name=self.name, reagent_roles=[], equipment_roles=[])
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# base_dict['reagent roles'] = []
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# base_dict['equipment roles'] = []
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for k, v in self.construct_xl_map_for_use(submission_type=submission_type):
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# logger.debug(f"Value: {v}")
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try:
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assoc = next(item for item in self.kit_reagentrole_associations if item.reagent_role.name == k)
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except StopIteration as e:
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@@ -280,10 +255,8 @@ class KitType(BaseClass):
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except StopIteration:
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continue
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for kk, vv in assoc.to_export_dict(extraction_kit=self).items():
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# logger.debug(f"{kk}:{vv}")
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v[kk] = vv
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base_dict['equipment_roles'].append(v)
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# logger.debug(f"KT returning {base_dict}")
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return base_dict
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@@ -347,28 +320,19 @@ class ReagentRole(BaseClass):
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else:
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match kit_type:
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case str():
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# logger.debug(f"Lookup ReagentType by kittype str {kit_type}")
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kit_type = KitType.query(name=kit_type)
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case _:
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pass
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match reagent:
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case str():
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# logger.debug(f"Lookup ReagentType by reagent str {reagent}")
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reagent = Reagent.query(lot=reagent)
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case _:
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pass
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assert reagent.role
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# logger.debug(f"Looking up reagent type for {type(kit_type)} {kit_type} and {type(reagent)} {reagent}")
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# logger.debug(f"Kit reagent types: {kit_type.reagent_types}")
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result = set(kit_type.reagent_roles).intersection(reagent.role)
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# logger.debug(f"Result: {result}")
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# try:
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return next((item for item in result), None)
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# except IndexError:
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# return None
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match name:
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case str():
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# logger.debug(f"Looking up reagent type by name str: {name}")
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query = query.filter(cls.name == name)
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limit = 1
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case _:
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@@ -457,7 +421,6 @@ class Reagent(BaseClass, LogMixin):
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rtype = reagent_role.name.replace("_", " ")
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except AttributeError:
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rtype = "Unknown"
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# logger.debug(f"Role for {self.name}: {rtype}")
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# NOTE: Calculate expiry with EOL from ReagentType
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try:
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place_holder = self.expiry + reagent_role.eol_ext
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@@ -493,14 +456,11 @@ class Reagent(BaseClass, LogMixin):
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Report: Result of operation
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"""
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report = Report()
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# logger.debug(f"Attempting update of last used reagent type at intersection of ({self}), ({kit})")
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rt = ReagentRole.query(kit_type=kit, reagent=self, limit=1)
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if rt is not None:
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# logger.debug(f"got reagenttype {rt}")
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assoc = KitTypeReagentRoleAssociation.query(kit_type=kit, reagent_role=rt)
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if assoc is not None:
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if assoc.last_used != self.lot:
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# logger.debug(f"Updating {assoc} last used to {self.lot}")
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assoc.last_used = self.lot
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result = assoc.save()
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report.add_result(result)
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@@ -539,23 +499,19 @@ class Reagent(BaseClass, LogMixin):
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pass
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match role:
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case str():
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# logger.debug(f"Looking up reagents by reagent type str: {reagent_type}")
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query = query.join(cls.role).filter(ReagentRole.name == role)
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case ReagentRole():
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# logger.debug(f"Looking up reagents by reagent type ReagentType: {reagent_type}")
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query = query.filter(cls.role.contains(role))
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case _:
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pass
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match name:
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case str():
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# logger.debug(f"Looking up reagent by name str: {name}")
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# NOTE: Not limited due to multiple reagents having same name.
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query = query.filter(cls.name == name)
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case _:
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pass
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match lot:
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case str():
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# logger.debug(f"Looking up reagent by lot number str: {lot}")
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query = query.filter(cls.lot == lot)
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# NOTE: In this case limit number returned.
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limit = 1
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@@ -579,7 +535,6 @@ class Reagent(BaseClass, LogMixin):
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case "expiry":
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if isinstance(value, str):
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field_value = datetime.strptime(value, "%Y-%m-%d")
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# field_value.replace(tzinfo=timezone)
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elif isinstance(value, date):
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field_value = datetime.combine(value, datetime.min.time())
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else:
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@@ -589,7 +544,6 @@ class Reagent(BaseClass, LogMixin):
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continue
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case _:
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field_value = value
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# logger.debug(f"Setting reagent {key} to {field_value}")
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self.__setattr__(key, field_value)
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self.save()
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@@ -634,25 +588,19 @@ class Discount(BaseClass):
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query: Query = cls.__database_session__.query(cls)
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match organization:
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case Organization():
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# logger.debug(f"Looking up discount with organization Organization: {organization}")
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query = query.filter(cls.client == Organization)
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case str():
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# logger.debug(f"Looking up discount with organization str: {organization}")
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query = query.join(Organization).filter(Organization.name == organization)
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case int():
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# logger.debug(f"Looking up discount with organization id: {organization}")
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query = query.join(Organization).filter(Organization.id == organization)
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case _:
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pass
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match kit_type:
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case KitType():
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# logger.debug(f"Looking up discount with kit type KitType: {kit_type}")
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query = query.filter(cls.kit == kit_type)
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case str():
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# logger.debug(f"Looking up discount with kit type str: {kit_type}")
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query = query.join(KitType).filter(KitType.name == kit_type)
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case int():
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# logger.debug(f"Looking up discount with kit type id: {kit_type}")
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query = query.join(KitType).filter(KitType.id == kit_type)
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case _:
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pass
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@@ -723,7 +671,6 @@ class SubmissionType(BaseClass):
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return submission_type.template_file
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def get_template_file_sheets(self) -> List[str]:
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logger.debug(f"Submission type to get sheets for: {self.name}")
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"""
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Gets names of sheet in the stored blank form.
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@@ -768,7 +715,6 @@ class SubmissionType(BaseClass):
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dict: Map of locations
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"""
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info = {k: v for k, v in self.info_map.items() if k != "custom"}
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logger.debug(f"Info map: {info}")
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match mode:
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case "read":
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output = {k: v[mode] for k, v in info.items() if v[mode]}
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@@ -844,11 +790,9 @@ class SubmissionType(BaseClass):
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"""
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match equipment_role:
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case str():
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# logger.debug(f"Getting processes for equipmentrole str {equipment_role}")
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relevant = [item.get_all_processes(kit) for item in self.submissiontype_equipmentrole_associations if
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item.equipment_role.name == equipment_role]
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case EquipmentRole():
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# logger.debug(f"Getting processes for equipmentrole EquipmentRole {equipment_role}")
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relevant = [item.get_all_processes(kit) for item in self.submissiontype_equipmentrole_associations if
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item.equipment_role == equipment_role]
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case _:
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@@ -886,14 +830,12 @@ class SubmissionType(BaseClass):
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query: Query = cls.__database_session__.query(cls)
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match name:
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case str():
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# logger.debug(f"Looking up submission type by name str: {name}")
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query = query.filter(cls.name == name)
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limit = 1
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case _:
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pass
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match key:
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case str():
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# logger.debug(f"Looking up submission type by info-map key str: {key}")
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query = query.filter(cls.info_map.op('->')(key) is not None)
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case _:
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pass
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@@ -946,7 +888,6 @@ class SubmissionType(BaseClass):
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import_dict = yaml.load(stream=f, Loader=yaml.Loader)
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else:
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raise Exception(f"Filetype {filepath.suffix} not supported.")
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# logger.debug(pformat(import_dict))
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try:
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submission_type = cls.query(name=import_dict['name'])
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except KeyError:
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@@ -1076,23 +1017,17 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
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query: Query = cls.__database_session__.query(cls)
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match submission_type:
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case SubmissionType():
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# logger.debug(f"Looking up {cls.__name__} by SubmissionType {submission_type}")
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query = query.filter(cls.submission_type == submission_type)
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case str():
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# logger.debug(f"Looking up {cls.__name__} by name {submission_type}")
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query = query.join(SubmissionType).filter(SubmissionType.name == submission_type)
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case int():
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# logger.debug(f"Looking up {cls.__name__} by id {submission_type}")
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query = query.join(SubmissionType).filter(SubmissionType.id == submission_type)
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match kit_type:
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case KitType():
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# logger.debug(f"Looking up {cls.__name__} by KitType {kit_type}")
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query = query.filter(cls.kit_type == kit_type)
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case str():
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# logger.debug(f"Looking up {cls.__name__} by name {kit_type}")
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query = query.join(KitType).filter(KitType.name == kit_type)
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case int():
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# logger.debug(f"Looking up {cls.__name__} by id {kit_type}")
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query = query.join(KitType).filter(KitType.id == kit_type)
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limit = query.count()
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return cls.execute_query(query=query, limit=limit)
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@@ -1107,7 +1042,6 @@ class SubmissionTypeKitTypeAssociation(BaseClass):
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exclude = ['_sa_instance_state', 'submission_types_id', 'kits_id', 'submission_type', 'kit_type']
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base_dict = {k: v for k, v in self.__dict__.items() if k not in exclude}
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base_dict['kit_type'] = self.kit_type.to_export_dict(submission_type=self.submission_type)
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# logger.debug(f"STKTA returning: {base_dict}")
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return base_dict
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@@ -1128,10 +1062,11 @@ class KitTypeReagentRoleAssociation(BaseClass):
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kit_type = relationship(KitType,
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back_populates="kit_reagentrole_associations") #: relationship to associated KitType
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# reference to the "ReagentType" object
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# NOTE: reference to the "ReagentType" object
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reagent_role = relationship(ReagentRole,
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back_populates="reagentrole_kit_associations") #: relationship to associated ReagentType
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# NOTE: reference to the "SubmissionType" object
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submission_type = relationship(SubmissionType,
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back_populates="submissiontype_kit_rt_associations") #: relationship to associated SubmissionType
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@@ -1203,19 +1138,15 @@ class KitTypeReagentRoleAssociation(BaseClass):
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query: Query = cls.__database_session__.query(cls)
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match kit_type:
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case KitType():
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# logger.debug(f"Lookup KitTypeReagentTypeAssociation by kit_type KitType {kit_type}")
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query = query.filter(cls.kit_type == kit_type)
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case str():
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# logger.debug(f"Lookup KitTypeReagentTypeAssociation by kit_type str {kit_type}")
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query = query.join(KitType).filter(KitType.name == kit_type)
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case _:
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pass
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match reagent_role:
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case ReagentRole():
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# logger.debug(f"Lookup KitTypeReagentTypeAssociation by reagent_type ReagentType {reagent_type}")
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query = query.filter(cls.reagent_role == reagent_role)
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case str():
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# logger.debug(f"Lookup KitTypeReagentTypeAssociation by reagent_type ReagentType {reagent_type}")
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query = query.join(ReagentRole).filter(ReagentRole.name == reagent_role)
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case _:
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pass
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@@ -1242,7 +1173,6 @@ class KitTypeReagentRoleAssociation(BaseClass):
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Returns:
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Generator: Generates of reagents.
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"""
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# logger.debug(f"Attempting lookup of reagents by type: {reagent.type}")
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reagents = self.reagent_role.instances
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try:
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regex = self.uses['exclude_regex']
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@@ -1309,7 +1239,6 @@ class SubmissionReagentAssociation(BaseClass):
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query: Query = cls.__database_session__.query(cls)
|
||||
match reagent:
|
||||
case Reagent() | str():
|
||||
# logger.debug(f"Lookup SubmissionReagentAssociation by reagent Reagent {reagent}")
|
||||
if isinstance(reagent, str):
|
||||
reagent = Reagent.query(lot=reagent)
|
||||
query = query.filter(cls.reagent == reagent)
|
||||
@@ -1319,10 +1248,8 @@ class SubmissionReagentAssociation(BaseClass):
|
||||
case BasicSubmission() | str():
|
||||
if isinstance(submission, str):
|
||||
submission = BasicSubmission.query(rsl_plate_num=submission)
|
||||
# logger.debug(f"Lookup SubmissionReagentAssociation by submission BasicSubmission {submission}")
|
||||
query = query.filter(cls.submission == submission)
|
||||
case int():
|
||||
# logger.debug(f"Lookup SubmissionReagentAssociation by submission id {submission}")
|
||||
submission = BasicSubmission.query(id=submission)
|
||||
query = query.join(BasicSubmission).filter(BasicSubmission.id == submission)
|
||||
case _:
|
||||
@@ -1439,21 +1366,18 @@ class Equipment(BaseClass, LogMixin):
|
||||
query = cls.__database_session__.query(cls)
|
||||
match name:
|
||||
case str():
|
||||
# logger.debug(f"Lookup Equipment by name str {name}")
|
||||
query = query.filter(cls.name == name)
|
||||
limit = 1
|
||||
case _:
|
||||
pass
|
||||
match nickname:
|
||||
case str():
|
||||
# logger.debug(f"Lookup Equipment by nickname str {nickname}")
|
||||
query = query.filter(cls.nickname == nickname)
|
||||
limit = 1
|
||||
case _:
|
||||
pass
|
||||
match asset_number:
|
||||
case str():
|
||||
# logger.debug(f"Lookup Equipment by asset_number str {asset_number}")
|
||||
query = query.filter(cls.asset_number == asset_number)
|
||||
limit = 1
|
||||
case _:
|
||||
@@ -1569,11 +1493,9 @@ class EquipmentRole(BaseClass):
|
||||
PydEquipmentRole: This EquipmentRole as PydEquipmentRole
|
||||
"""
|
||||
from backend.validators.pydant import PydEquipmentRole
|
||||
# logger.debug("Creating list of PydEquipment in this role")
|
||||
equipment = [item.to_pydantic(submission_type=submission_type, extraction_kit=extraction_kit) for item in
|
||||
self.instances]
|
||||
pyd_dict = self.to_dict()
|
||||
# logger.debug("Creating list of Processes in this role")
|
||||
pyd_dict['processes'] = self.get_processes(submission_type=submission_type, extraction_kit=extraction_kit)
|
||||
return PydEquipmentRole(equipment=equipment, **pyd_dict)
|
||||
|
||||
@@ -1595,14 +1517,12 @@ class EquipmentRole(BaseClass):
|
||||
query = cls.__database_session__.query(cls)
|
||||
match id:
|
||||
case int():
|
||||
# logger.debug(f"Lookup EquipmentRole by id {id}")
|
||||
query = query.filter(cls.id == id)
|
||||
limit = 1
|
||||
case _:
|
||||
pass
|
||||
match name:
|
||||
case str():
|
||||
# logger.debug(f"Lookup EquipmentRole by name str {name}")
|
||||
query = query.filter(cls.name == name)
|
||||
limit = 1
|
||||
case _:
|
||||
@@ -1622,7 +1542,6 @@ class EquipmentRole(BaseClass):
|
||||
List[Process]: List of processes
|
||||
"""
|
||||
if isinstance(submission_type, str):
|
||||
# logger.debug(f"Checking if str {submission_type} exists")
|
||||
submission_type = SubmissionType.query(name=submission_type)
|
||||
if isinstance(extraction_kit, str):
|
||||
extraction_kit = KitType.query(name=extraction_kit)
|
||||
@@ -1808,7 +1727,6 @@ class Process(BaseClass):
|
||||
query = cls.__database_session__.query(cls)
|
||||
match name:
|
||||
case str():
|
||||
# logger.debug(f"Lookup Process with name str {name}")
|
||||
query = query.filter(cls.name == name)
|
||||
limit = 1
|
||||
case _:
|
||||
@@ -1892,13 +1810,11 @@ class Tips(BaseClass, LogMixin):
|
||||
query = cls.__database_session__.query(cls)
|
||||
match name:
|
||||
case str():
|
||||
# logger.debug(f"Lookup Equipment by name str {name}")
|
||||
query = query.filter(cls.name == name)
|
||||
case _:
|
||||
pass
|
||||
match lot:
|
||||
case str():
|
||||
# logger.debug(f"Lookup Equipment by nickname str {nickname}")
|
||||
query = query.filter(cls.lot == lot)
|
||||
limit = 1
|
||||
case _:
|
||||
|
||||
Reference in New Issue
Block a user