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Renaming ReagentType to ReagentRole

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This commit is contained in:
lwark
2024-06-07 14:15:19 -05:00
parent a355c5bb76
commit c7b6c90eac
8 changed files with 197 additions and 129 deletions
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56
src/submissions/backend/db/models/submissions.py
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@@ -248,6 +248,7 @@ class BasicSubmission(BaseClass):
ext_info = self.extraction_info
except TypeError:
ext_info = None
output = {
"id": self.id,
"plate_number": self.rsl_plate_num,
@@ -257,8 +258,7 @@ class BasicSubmission(BaseClass):
"submitting_lab": sub_lab,
"sample_count": self.sample_count,
"extraction_kit": ext_kit,
"cost": self.run_cost,
"cost": self.run_cost
}
if report:
return output
@@ -299,6 +299,15 @@ class BasicSubmission(BaseClass):
except Exception as e:
logger.error(f"Error setting comment: {self.comment}, {e}")
comments = None
try:
contact = self.contact.name
except AttributeError as e:
logger.error(f"Problem setting contact: {e}")
contact = "NA"
try:
contact_phone = self.contact.phone
except AttributeError:
contact_phone = "NA"
output["submission_category"] = self.submission_category
output["technician"] = self.technician
output["reagents"] = reagents
@@ -308,9 +317,9 @@ class BasicSubmission(BaseClass):
output["equipment"] = equipment
output["cost_centre"] = cost_centre
output["signed_by"] = self.signed_by
output["contact"] = self.contact.name
output["contact_phone"] = self.contact.phone
# logger.debug(f"Setting contact to: {contact} of type: {type(contact)}")
output["contact"] = contact
output["contact_phone"] = contact_phone
return output
def calculate_column_count(self) -> int:
@@ -431,7 +440,7 @@ class BasicSubmission(BaseClass):
excluded = ['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']
'signed_by', 'artic_date', 'gel_barcode', 'gel_date', 'ngs_date', 'contact_phone', 'contact']
for item in excluded:
try:
df = df.drop(item, axis=1)
@@ -544,7 +553,6 @@ class BasicSubmission(BaseClass):
# logger.debug("To dict complete")
new_dict = {}
for key, value in dicto.items():
# start = time()
# logger.debug(f"Checking {key}")
missing = value is None or value in ['', 'None']
match key:
@@ -1403,6 +1411,10 @@ class WastewaterArtic(BasicSubmission):
gel_info = Column(JSON) #: unstructured data from gel.
gel_controls = Column(JSON) #: locations of controls on the gel
source_plates = Column(JSON) #: wastewater plates that samples come from
artic_date = Column(TIMESTAMP) #: Date Artic Performed
ngs_date = Column(TIMESTAMP) #: Date submission received
gel_date = Column(TIMESTAMP) #: Date submission received
gel_barcode = Column(String(16))
__mapper_args__ = dict(polymorphic_identity="Wastewater Artic",
polymorphic_load="inline",
@@ -1418,12 +1430,18 @@ class WastewaterArtic(BasicSubmission):
output = super().to_dict(full_data=full_data, backup=backup, report=report)
if self.artic_technician in [None, "None"]:
output['artic_technician'] = self.technician
else:
output['artic_technician'] = self.artic_technician
if report:
return output
output['gel_info'] = self.gel_info
output['gel_image'] = self.gel_image
output['dna_core_submission_number'] = self.dna_core_submission_number
output['source_plates'] = self.source_plates
output['artic_date'] = self.artic_date or self.submitted_date
output['ngs_date'] = self.ngs_date or self.submitted_date
output['gel_date'] = self.gel_date or self.submitted_date
output['gel_barcode'] = self.gel_barcode
return output
@classmethod
@@ -1756,19 +1774,22 @@ class WastewaterArtic(BasicSubmission):
output.append(dicto)
continue
for item in self.source_plates:
old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
if assoc.sample.id is None:
old_plate = None
else:
old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
if old_plate is not None:
set_plate = old_plate.submission.rsl_plate_num
logger.debug(dicto['WW Processing Num'])
if dicto['WW Processing Num'].startswith("NTC"):
dicto['Well'] = dicto['WW Processing Num']
# logger.debug(f"Dictionary: {pformat(dicto)}")
if dicto['ww_processing_num'].startswith("NTC"):
dicto['well'] = dicto['ww_processing_num']
else:
dicto['Well'] = f"{row_map[old_plate.row]}{old_plate.column}"
dicto['well'] = f"{row_map[old_plate.row]}{old_plate.column}"
break
elif dicto['WW Processing Num'].startswith("NTC"):
dicto['Well'] = dicto['WW Processing Num']
elif dicto['ww_processing_num'].startswith("NTC"):
dicto['well'] = dicto['ww_processing_num']
dicto['plate_name'] = set_plate
logger.debug(f"Here is our raw sample: {pformat(dicto)}")
# logger.debug(f"Here is our raw sample: {pformat(dicto)}")
output.append(dicto)
return output
@@ -1801,7 +1822,7 @@ class WastewaterArtic(BasicSubmission):
fname = select_open_file(obj=obj, file_extension="jpg")
dlg = GelBox(parent=obj, img_path=fname, submission=self)
if dlg.exec():
self.dna_core_submission_number, img_path, output, comment = dlg.parse_form()
self.dna_core_submission_number, self.gel_barcode, img_path, output, comment = dlg.parse_form()
self.gel_image = img_path.name
self.gel_info = output
dt = datetime.strftime(datetime.now(), "%Y-%m-%d %H:%M:%S")
@@ -2135,7 +2156,7 @@ class BasicSample(BaseClass):
if dlg.exec():
pass
#Below are the custom sample types
# Below are the custom sample types
class WastewaterSample(BasicSample):
"""
@@ -2235,6 +2256,7 @@ class WastewaterSample(BasicSample):
searchables.append(dict(label=label, field=item))
return searchables
class BacterialCultureSample(BasicSample):
"""
base of bacterial culture sample