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Created WastewaterArticAssociation, added tip handling.

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This commit is contained in:
lwark
2024-06-14 10:38:46 -05:00
parent 4a7d0b0bd4
commit 62b826c2d1
7 changed files with 163 additions and 59 deletions
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2
src/submissions/backend/db/models/kits.py
View File

@@ -1601,7 +1601,7 @@ class SubmissionTipsAssociation(BaseClass):
back_populates="submission_tips_associations") #: associated submission
tips = relationship(Tips,
back_populates="tips_submission_associations") #: associated equipment
role_name = Column(String(32)) #, ForeignKey("_tiprole.name"))
role_name = Column(String(32), primary_key=True) #, ForeignKey("_tiprole.name"))
# role = relationship(TipRole)

6
src/submissions/backend/db/models/submissions.py
View File

@@ -2095,7 +2095,7 @@ class BasicSample(BaseClass):
used_class = cls.find_polymorphic_subclass(attrs=sanitized_kwargs, polymorphic_identity=sample_type)
instance = used_class(**sanitized_kwargs)
instance.sample_type = sample_type
logger.debug(f"Creating instance: {instance}")
# logger.debug(f"Creating instance: {instance}")
return instance
@classmethod
@@ -2352,7 +2352,7 @@ class SubmissionSampleAssociation(BaseClass):
self.id = id
else:
self.id = self.__class__.autoincrement_id()
logger.debug(f"Looking at kwargs: {pformat(kwargs)}")
# logger.debug(f"Looking at kwargs: {pformat(kwargs)}")
for k,v in kwargs.items():
try:
self.__setattr__(k, v)
@@ -2538,7 +2538,7 @@ class SubmissionSampleAssociation(BaseClass):
Returns:
SubmissionSampleAssociation: Queried or new association.
"""
logger.debug(f"Attempting create or query with {kwargs}")
# logger.debug(f"Attempting create or query with {kwargs}")
match submission:
case BasicSubmission():
pass

2
src/submissions/backend/excel/parser.py
View File

@@ -613,7 +613,7 @@ class EquipmentParser(object):
previous_asset = asset
asset = self.get_asset_number(input=asset)
logger.debug(f"asset: {asset}")
eq = Equipment.query(name=asset)
eq = Equipment.query(asset_number=asset)
process = ws.cell(row=v['process']['row'], column=v['process']['column']).value
try:
output.append(

138
src/submissions/backend/excel/writer.py
View File

@@ -15,7 +15,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
class SheetWriter(object):
"""
object to pull and contain data from excel file
object to manage data placement into excel file
"""
def __init__(self, submission: PydSubmission, missing_only: bool = False):
@@ -60,35 +60,52 @@ class SheetWriter(object):
self.write_tips()
def write_info(self):
"""
Calls info writer
"""
disallowed = ['filepath', 'reagents', 'samples', 'equipment', 'controls']
info_dict = {k: v for k, v in self.sub.items() if k not in disallowed}
writer = InfoWriter(xl=self.xl, submission_type=self.submission_type, info_dict=info_dict)
self.xl = writer.write_info()
def write_reagents(self):
"""
Calls reagent writer
"""
reagent_list = self.sub['reagents']
writer = ReagentWriter(xl=self.xl, submission_type=self.submission_type,
extraction_kit=self.sub['extraction_kit'], reagent_list=reagent_list)
self.xl = writer.write_reagents()
def write_samples(self):
"""
Calls sample writer
"""
sample_list = self.sub['samples']
writer = SampleWriter(xl=self.xl, submission_type=self.submission_type, sample_list=sample_list)
self.xl = writer.write_samples()
def write_equipment(self):
"""
Calls equipment writer
"""
equipment_list = self.sub['equipment']
writer = EquipmentWriter(xl=self.xl, submission_type=self.submission_type, equipment_list=equipment_list)
self.xl = writer.write_equipment()
def write_tips(self):
"""
Calls tip writer
"""
tips_list = self.sub['tips']
writer = TipWriter(xl=self.xl, submission_type=self.submission_type, tips_list=tips_list)
self.xl = writer.write_tips()
class InfoWriter(object):
"""
object to write general submission info into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, info_dict: dict, sub_object:BasicSubmission|None=None):
logger.debug(f"Info_dict coming into InfoWriter: {pformat(info_dict)}")
if isinstance(submission_type, str):
@@ -103,6 +120,16 @@ class InfoWriter(object):
# logger.debug(pformat(self.info))
def reconcile_map(self, info_dict: dict, info_map: dict) -> dict:
"""
Merge info with its locations
Args:
info_dict (dict): dictionary of info items
info_map (dict): dictionary of info locations
Returns:
dict: merged dictionary
"""
output = {}
for k, v in info_dict.items():
if v is None:
@@ -119,7 +146,13 @@ class InfoWriter(object):
# logger.debug(f"Reconciled info: {pformat(output)}")
return output
def write_info(self):
def write_info(self) -> Workbook:
"""
Performs write operations
Returns:
Workbook: workbook with info written.
"""
for k, v in self.info.items():
# NOTE: merge all comments to fit in single cell.
if k == "comment" and isinstance(v['value'], list):
@@ -138,7 +171,9 @@ class InfoWriter(object):
class ReagentWriter(object):
"""
object to write reagent data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, extraction_kit: KitType | str,
reagent_list: list):
self.xl = xl
@@ -149,7 +184,17 @@ class ReagentWriter(object):
reagent_map = kit_type.construct_xl_map_for_use(submission_type)
self.reagents = self.reconcile_map(reagent_list=reagent_list, reagent_map=reagent_map)
def reconcile_map(self, reagent_list, reagent_map) -> List[dict]:
def reconcile_map(self, reagent_list:List[dict], reagent_map:dict) -> List[dict]:
"""
Merge reagents with their locations
Args:
reagent_list (List[dict]): List of reagent dictionaries
reagent_map (dict): Reagent locations
Returns:
List[dict]: merged dictionary
"""
output = []
for reagent in reagent_list:
try:
@@ -168,7 +213,13 @@ class ReagentWriter(object):
output.append(placeholder)
return output
def write_reagents(self):
def write_reagents(self) -> Workbook:
"""
Performs write operations
Returns:
Workbook: Workbook with reagents written
"""
for reagent in self.reagents:
sheet = self.xl[reagent['sheet']]
for k, v in reagent.items():
@@ -181,7 +232,9 @@ class ReagentWriter(object):
class SampleWriter(object):
"""
object to write sample data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, sample_list: list):
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -190,7 +243,16 @@ class SampleWriter(object):
self.sample_map = submission_type.construct_sample_map()['lookup_table']
self.samples = self.reconcile_map(sample_list)
def reconcile_map(self, sample_list: list):
def reconcile_map(self, sample_list: list) -> List[dict]:
"""
Merge sample info with locations
Args:
sample_list (list): List of sample information
Returns:
List[dict]: List of merged dictionaries
"""
output = []
multiples = ['row', 'column', 'assoc_id', 'submission_rank']
for sample in sample_list:
@@ -204,10 +266,16 @@ class SampleWriter(object):
output.append(new)
return sorted(output, key=lambda k: k['submission_rank'])
def write_samples(self):
def write_samples(self) -> Workbook:
"""
Performs writing operations.
Returns:
Workbook: Workbook with samples written
"""
sheet = self.xl[self.sample_map['sheet']]
columns = self.sample_map['sample_columns']
for ii, sample in enumerate(self.samples):
for sample in self.samples:
row = self.sample_map['start_row'] + (sample['submission_rank'] - 1)
for k, v in sample.items():
try:
@@ -219,7 +287,9 @@ class SampleWriter(object):
class EquipmentWriter(object):
"""
object to write equipment data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, equipment_list: list):
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -228,7 +298,17 @@ class EquipmentWriter(object):
equipment_map = self.submission_type.construct_equipment_map()
self.equipment = self.reconcile_map(equipment_list=equipment_list, equipment_map=equipment_map)
def reconcile_map(self, equipment_list: list, equipment_map: list):
def reconcile_map(self, equipment_list: list, equipment_map: dict) -> List[dict]:
"""
Merges equipment with location data
Args:
equipment_list (list): List of equipment
equipment_map (dict): Dictionary of equipment locations
Returns:
List[dict]: List of merged dictionaries
"""
output = []
if equipment_list is None:
return output
@@ -248,6 +328,8 @@ class EquipmentWriter(object):
# logger.error(f"Keyerror: {e}")
continue
placeholder[k] = dicto
if "asset_number" not in mp_info.keys():
placeholder['name']['value'] = f"{equipment['name']} - {equipment['asset_number']}"
try:
placeholder['sheet'] = mp_info['sheet']
except KeyError:
@@ -256,7 +338,13 @@ class EquipmentWriter(object):
output.append(placeholder)
return output
def write_equipment(self):
def write_equipment(self) -> Workbook:
"""
Performs write operations
Returns:
Workbook: Workbook with equipment written
"""
for equipment in self.equipment:
try:
sheet = self.xl[equipment['sheet']]
@@ -280,7 +368,9 @@ class EquipmentWriter(object):
class TipWriter(object):
"""
object to write tips data into excel file
"""
def __init__(self, xl: Workbook, submission_type: SubmissionType | str, tips_list: list):
if isinstance(submission_type, str):
submission_type = SubmissionType.query(name=submission_type)
@@ -289,7 +379,17 @@ class TipWriter(object):
tips_map = self.submission_type.construct_tips_map()
self.tips = self.reconcile_map(tips_list=tips_list, tips_map=tips_map)
def reconcile_map(self, tips_list: list, tips_map: list):
def reconcile_map(self, tips_list: List[dict], tips_map: dict) -> List[dict]:
"""
Merges tips with location data
Args:
tips_list (List[dict]): List of tips
tips_map (dict): Tips locations
Returns:
List[dict]: List of merged dictionaries
"""
output = []
if tips_list is None:
return output
@@ -317,7 +417,13 @@ class TipWriter(object):
output.append(placeholder)
return output
def write_tips(self):
def write_tips(self) -> Workbook:
"""
Performs write operations
Returns:
Workbook: Workbook with tips written
"""
for tips in self.tips:
try:
sheet = self.xl[tips['sheet']]

3
src/submissions/backend/validators/pydant.py
View File

@@ -257,7 +257,7 @@ class PydSample(BaseModel, extra='allow'):
sample=instance,
row=row, column=column, id=aid,
submission_rank=submission_rank, **self.model_extra)
logger.debug(f"Using submission_sample_association: {association}")
# logger.debug(f"Using submission_sample_association: {association}")
try:
# instance.sample_submission_associations.append(association)
out_associations.append(association)
@@ -734,6 +734,7 @@ class PydSubmission(BaseModel, extra='allow'):
for tips in self.tips:
if tips is None:
continue
logger.debug(f"Converting tips: {tips} to sql.")
association = tips.to_sql(submission=instance)
if association is not None:
# association.save()