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Pydantic added for validation.

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This commit is contained in:
Landon Wark
2023-07-07 14:27:26 -05:00
parent 0c81c74f70
commit 1c804bfc6a
12 changed files with 497 additions and 141 deletions
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9
src/submissions/tools/__init__.py
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@@ -24,6 +24,8 @@ def check_not_nan(cell_contents) -> bool:
# check for nan as a string first
if cell_contents == 'nan':
cell_contents = np.nan
if cell_contents == None:
cell_contents = np.nan
try:
return not np.isnan(cell_contents)
except TypeError:
@@ -81,14 +83,15 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
# What type is sub?
match sub:
case BasicSubmission():
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
# very hacky method to ensure interchangeable plates are not
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types if reagenttype.required == 1]
# Overwrite function parameter reagenttypes
try:
reagenttypes = [reagent.type.name for reagent in sub.reagents]
except AttributeError as e:
logger.error(f"Problem parsing reagents: {[f'{reagent.lot}, {reagent.type}' for reagent in sub.reagents]}")
case KitType():
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types]
ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types if reagenttype.required == 1]
logger.debug(f"Kit reagents: {ext_kit_rtypes}")
logger.debug(f"Submission reagents: {reagenttypes}")
# check if lists are equal
@@ -256,7 +259,7 @@ class RSLNamer(object):
def massage_common_reagents(reagent_name:str):
logger.debug(f"Attempting to massage {reagent_name}")
if reagent_name.endswith("water") or "H2O" in reagent_name:
if reagent_name.endswith("water") or "H2O" in reagent_name.upper():
reagent_name = "molecular_grade_water"
reagent_name = reagent_name.replace("µ", "u")
return reagent_name