Bug fixes.
This commit is contained in:
lwark
@@ -295,8 +295,10 @@ class BasicSubmission(BaseClass):
|
||||
if k == 'info':
|
||||
continue
|
||||
if not any([item['role'] == k for item in reagents]):
|
||||
# expiry = date(year=1970, month=1, day=1)
|
||||
expiry = "NA"
|
||||
reagents.append(
|
||||
dict(role=k, name="Not Applicable", lot="NA", expiry=date(year=1970, month=1, day=1),
|
||||
dict(role=k, name="Not Applicable", lot="NA", expiry=expiry,
|
||||
missing=True))
|
||||
except Exception as e:
|
||||
logger.error(f"We got an error retrieving reagents: {e}")
|
||||
@@ -507,10 +509,10 @@ class BasicSubmission(BaseClass):
|
||||
sample, _ = sample.to_sql(submission=self)
|
||||
return
|
||||
case "reagents":
|
||||
logger.debug(f"Reagents coming into SQL: {value}")
|
||||
# logger.debug(f"Reagents coming into SQL: {value}")
|
||||
field_value = [reagent['value'].to_sql()[0] if isinstance(reagent, dict) else reagent.to_sql()[0] for
|
||||
reagent in value]
|
||||
logger.debug(f"Reagents coming out of SQL: {field_value}")
|
||||
# logger.debug(f"Reagents coming out of SQL: {field_value}")
|
||||
case "submission_type":
|
||||
field_value = SubmissionType.query(name=value)
|
||||
case "sample_count":
|
||||
@@ -521,7 +523,7 @@ class BasicSubmission(BaseClass):
|
||||
case "ctx" | "csv" | "filepath" | "equipment":
|
||||
return
|
||||
case item if item in self.jsons():
|
||||
logger.debug(f"Setting JSON attribute.")
|
||||
# logger.debug(f"Setting JSON attribute.")
|
||||
existing = self.__getattribute__(key)
|
||||
if value is None or value in ['', 'null']:
|
||||
logger.error(f"No value given, not setting.")
|
||||
@@ -617,7 +619,7 @@ class BasicSubmission(BaseClass):
|
||||
Args:
|
||||
original (bool, optional): Is this the first save. Defaults to True.
|
||||
"""
|
||||
logger.debug("Saving submission.")
|
||||
# logger.debug("Saving submission.")
|
||||
if original:
|
||||
self.uploaded_by = getuser()
|
||||
super().save()
|
||||
@@ -1177,9 +1179,12 @@ class BasicSubmission(BaseClass):
|
||||
# logger.debug(f"Processing: {equip}")
|
||||
_, assoc = equip.toSQL(submission=self)
|
||||
# logger.debug(f"Appending SubmissionEquipmentAssociation: {assoc}")
|
||||
assoc.save()
|
||||
try:
|
||||
assoc.save()
|
||||
except AttributeError as e:
|
||||
logger.error(f"Couldn't save association with {equip} due to {e}")
|
||||
if equip.tips:
|
||||
logger.debug("We have tips in this equipment")
|
||||
# logger.debug("We have tips in this equipment")
|
||||
for tips in equip.tips:
|
||||
tassoc = tips.to_sql(submission=self)
|
||||
tassoc.save()
|
||||
@@ -1308,7 +1313,7 @@ class BacterialCulture(BasicSubmission):
|
||||
idx = df[df[0] == sample.well]
|
||||
if idx.empty:
|
||||
new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
|
||||
logger.debug(f"Checking: {new}")
|
||||
# logger.debug(f"Checking: {new}")
|
||||
idx = df[df[0] == new]
|
||||
# logger.debug(f"Here is the row: {idx}")
|
||||
row = idx.index.to_list()[0]
|
||||
@@ -1366,7 +1371,7 @@ class Wastewater(BasicSubmission):
|
||||
dict: Updated sample dictionary
|
||||
"""
|
||||
input_dict = super().custom_info_parser(input_dict)
|
||||
logger.debug(f"Input dict: {pformat(input_dict)}")
|
||||
# logger.debug(f"Input dict: {pformat(input_dict)}")
|
||||
if xl is not None:
|
||||
try:
|
||||
input_dict['csv'] = xl["Copy to import file"]
|
||||
@@ -1636,12 +1641,14 @@ class WastewaterArtic(BasicSubmission):
|
||||
input_dict = super().custom_info_parser(input_dict)
|
||||
egel_section = custom_fields['egel_results']
|
||||
ws = xl[egel_section['sheet']]
|
||||
data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']) for
|
||||
ii in range(egel_section['start_row'], egel_section['end_row'])]
|
||||
data = [ws.cell(row=ii, column=jj) for jj in range(egel_section['start_column'], egel_section['end_column']+1) for
|
||||
ii in range(egel_section['start_row'], egel_section['end_row']+1)]
|
||||
data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
|
||||
# logger.debug(f"Got gel control map: {data}")
|
||||
input_dict['gel_controls'] = [
|
||||
dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in
|
||||
data]
|
||||
# logger.debug(f"Got gel control info: {input_dict['gel_controls']}")
|
||||
# NOTE: Get source plate information
|
||||
source_plates_section = custom_fields['source_plates']
|
||||
ws = xl[source_plates_section['sheet']]
|
||||
@@ -1854,10 +1861,10 @@ class WastewaterArtic(BasicSubmission):
|
||||
"""
|
||||
input_excel = super().custom_info_writer(input_excel, info, backup)
|
||||
if isinstance(info, types.GeneratorType):
|
||||
logger.debug(f"Unpacking info generator.")
|
||||
# logger.debug(f"Unpacking info generator.")
|
||||
info = {k: v for k, v in info}
|
||||
logger.debug(f"Info:\n{pformat(info)}")
|
||||
logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
|
||||
# logger.debug(f"Info:\n{pformat(info)}")
|
||||
# logger.debug(f"Custom fields:\n{pformat(custom_fields)}")
|
||||
# NOTE: check for source plate information
|
||||
if check_key_or_attr(key='source_plates', interest=info, check_none=True):
|
||||
source_plates_section = custom_fields['source_plates']
|
||||
@@ -2016,7 +2023,7 @@ class WastewaterArtic(BasicSubmission):
|
||||
img = zipped.read(input_dict['gel_image_path'])
|
||||
with tempfile.TemporaryFile(mode="wb", suffix=".jpg", delete=False) as tmp:
|
||||
tmp.write(img)
|
||||
logger.debug(f"Tempfile: {tmp.name}")
|
||||
# logger.debug(f"Tempfile: {tmp.name}")
|
||||
img = InlineImage(tpl_obj, image_descriptor=tmp.name, width=Inches(5.5)) #, width=5.5)#, height=400)
|
||||
input_dict['gel_image'] = img
|
||||
return input_dict
|
||||
|
||||
Reference in New Issue
Block a user