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Various bug fixes for new forms.

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This commit is contained in:
Landon Wark
2024-04-25 08:55:32 -05:00
parent 5466c78c3a
commit 8cc161ec56
18 changed files with 520 additions and 218 deletions
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43
src/submissions/backend/excel/parser.py
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@@ -62,9 +62,11 @@ class SheetParser(object):
parser = InfoParser(xl=self.xl, submission_type=self.sub['submission_type']['value'])
info = parser.parse_info()
self.info_map = parser.map
# exclude_from_info = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.sub['submission_type']).exclude_from_info_parser()
for k,v in info.items():
match k:
case "sample":
# case item if
pass
case _:
self.sub[k] = v
@@ -97,9 +99,9 @@ class SheetParser(object):
"""
Enforce that the parser has an extraction kit
"""
from frontend.widgets.pop_ups import KitSelector
from frontend.widgets.pop_ups import ObjectSelector
if not check_not_nan(self.sub['extraction_kit']['value']):
dlg = KitSelector(title="Kit Needed", message="At minimum a kit is needed. Please select one.")
dlg = ObjectSelector(title="Kit Needed", message="At minimum a kit is needed. Please select one.", obj_type=KitType)
if dlg.exec():
self.sub['extraction_kit'] = dict(value=dlg.getValues(), missing=True)
else:
@@ -133,7 +135,11 @@ class SheetParser(object):
"""
# logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
logger.debug(f"Equipment: {self.sub['equipment']}")
if len(self.sub['equipment']) == 0:
try:
check = len(self.sub['equipment']) == 0
except TypeError:
check = True
if check:
self.sub['equipment'] = None
psm = PydSubmission(filepath=self.filepath, **self.sub)
return psm
@@ -142,11 +148,12 @@ class InfoParser(object):
def __init__(self, xl:pd.ExcelFile, submission_type:str):
logger.info(f"\n\Hello from InfoParser!\n\n")
self.map = self.fetch_submission_info_map(submission_type=submission_type)
self.submission_type = submission_type
self.map = self.fetch_submission_info_map()
self.xl = xl
logger.debug(f"Info map for InfoParser: {pformat(self.map)}")
def fetch_submission_info_map(self, submission_type:str|dict) -> dict:
def fetch_submission_info_map(self) -> dict:
"""
Gets location of basic info from the submission_type object in the database.
@@ -156,10 +163,10 @@ class InfoParser(object):
Returns:
dict: Location map of all info for this submission type
"""
if isinstance(submission_type, str):
submission_type = dict(value=submission_type, missing=True)
logger.debug(f"Looking up submission type: {submission_type['value']}")
submission_type = SubmissionType.query(name=submission_type['value'])
if isinstance(self.submission_type, str):
self.submission_type = dict(value=self.submission_type, missing=True)
logger.debug(f"Looking up submission type: {self.submission_type['value']}")
submission_type = SubmissionType.query(name=self.submission_type['value'])
info_map = submission_type.info_map
# Get the parse_info method from the submission type specified
self.custom_parser = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=submission_type.name).parse_info
@@ -172,16 +179,25 @@ class InfoParser(object):
Returns:
dict: key:value of basic info
"""
if isinstance(self.submission_type, str):
self.submission_type = dict(value=self.submission_type, missing=True)
dicto = {}
exclude_from_generic = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type['value']).get_default_info("parser_ignore")
# This loop parses generic info
logger.debug(f"Map: {self.map}")
# time.sleep(5)
for sheet in self.xl.sheet_names:
df = self.xl.parse(sheet, header=None)
relevant = {}
for k, v in self.map.items():
# exclude from generic parsing
if k in exclude_from_generic:
continue
# If the value is hardcoded put it in the dictionary directly.
if isinstance(v, str):
dicto[k] = dict(value=v, missing=False)
continue
if k in ["samples", "all_sheets"]:
continue
logger.debug(f"Looking for {k} in self.map")
if sheet in self.map[k]['sheets']:
relevant[k] = v
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
@@ -252,6 +268,7 @@ class ReagentParser(object):
lot = df.iat[relevant[item]['lot']['row']-1, relevant[item]['lot']['column']-1]
expiry = df.iat[relevant[item]['expiry']['row']-1, relevant[item]['expiry']['column']-1]
if 'comment' in relevant[item].keys():
logger.debug(f"looking for {relevant[item]} comment.")
comment = df.iat[relevant[item]['comment']['row']-1, relevant[item]['comment']['column']-1]
else:
comment = ""
@@ -294,7 +311,7 @@ class SampleParser(object):
sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
logger.debug(f"sample_info_map: {sample_info_map}")
self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map'])
logger.debug(f"plate_map: {self.plate_map}")
# logger.debug(f"plate_map: {self.plate_map}")
self.lookup_table = self.construct_lookup_table(lookup_table_location=sample_info_map['lookup_table'])
if "plates" in sample_info_map:
self.plates = sample_info_map['plates']
@@ -439,7 +456,7 @@ class SampleParser(object):
"""
result = None
new_samples = []
logger.debug(f"Starting samples: {pformat(self.samples)}")
# logger.debug(f"Starting samples: {pformat(self.samples)}")
for sample in self.samples:
translated_dict = {}
for k, v in sample.items():