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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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6
src/submissions/backend/excel/parser.py
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@@ -139,7 +139,7 @@ class SheetParser(object):
# logger.debug(f"Submission dictionary coming into 'to_pydantic':\n{pformat(self.sub)}")
pyd_dict = copy(self.sub)
pyd_dict['samples'] = [PydSample(**sample) for sample in self.sub['samples']]
logger.debug(f"Reagents: {pformat(self.sub['reagents'])}")
# logger.debug(f"Reagents: {pformat(self.sub['reagents'])}")
pyd_dict['reagents'] = [PydReagent(**reagent) for reagent in self.sub['reagents']]
# logger.debug(f"Equipment: {self.sub['equipment']}")
try:
@@ -215,13 +215,13 @@ class InfoParser(object):
new = location
new['name'] = k
relevant.append(new)
logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
# logger.debug(f"relevant map for {sheet}: {pformat(relevant)}")
if not relevant:
continue
for item in relevant:
# NOTE: Get cell contents at this location
value = ws.cell(row=item['row'], column=item['column']).value
logger.debug(f"Value for {item['name']} = {value}")
# logger.debug(f"Value for {item['name']} = {value}")
match item['name']:
case "submission_type":
value, missing = is_missing(value)

47
src/submissions/backend/excel/writer.py
View File

@@ -53,7 +53,8 @@ class SheetWriter(object):
template = self.submission_type.template_file
workbook = load_workbook(BytesIO(template))
missing_only = False
self.workbook = workbook
# self.workbook = workbook
self.xl = workbook
self.write_info()
self.write_reagents()
self.write_samples()
@@ -62,23 +63,23 @@ class SheetWriter(object):
def write_info(self):
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.workbook, submission_type=self.submission_type, info_dict=info_dict)
writer = InfoWriter(xl=self.xl, submission_type=self.submission_type, info_dict=info_dict)
self.xl = writer.write_info()
def write_reagents(self):
reagent_list = self.sub['reagents']
writer = ReagentWriter(xl=self.workbook, submission_type=self.submission_type,
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):
sample_list = self.sub['samples']
writer = SampleWriter(xl=self.workbook, submission_type=self.submission_type, sample_list=sample_list)
writer = SampleWriter(xl=self.xl, submission_type=self.submission_type, sample_list=sample_list)
self.xl = writer.write_samples()
def write_equipment(self):
equipment_list = self.sub['equipment']
writer = EquipmentWriter(xl=self.workbook, submission_type=self.submission_type, equipment_list=equipment_list)
writer = EquipmentWriter(xl=self.xl, submission_type=self.submission_type, equipment_list=equipment_list)
self.xl = writer.write_equipment()
@@ -93,18 +94,18 @@ class InfoWriter(object):
self.submission_type = submission_type
self.sub_object = sub_object
self.xl = xl
map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, map)
info_map = submission_type.construct_info_map(mode='write')
self.info = self.reconcile_map(info_dict, info_map)
# logger.debug(pformat(self.info))
def reconcile_map(self, info_dict: dict, map: dict) -> dict:
def reconcile_map(self, info_dict: dict, info_map: dict) -> dict:
output = {}
for k, v in info_dict.items():
if v is None:
continue
dicto = {}
try:
dicto['locations'] = map[k]
dicto['locations'] = info_map[k]
except KeyError:
# continue
pass
@@ -126,7 +127,7 @@ class InfoWriter(object):
logger.error(f"No locations for {k}, skipping")
continue
for loc in locations:
# logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
logger.debug(f"Writing {k} to {loc['sheet']}, row: {loc['row']}, column: {loc['column']}")
sheet = self.xl[loc['sheet']]
sheet.cell(row=loc['row'], column=loc['column'], value=v['value'])
return self.sub_object.custom_info_writer(self.xl, info=self.info)
@@ -141,14 +142,14 @@ class ReagentWriter(object):
submission_type = SubmissionType.query(name=submission_type)
if isinstance(extraction_kit, str):
kit_type = KitType.query(name=extraction_kit)
map = kit_type.construct_xl_map_for_use(submission_type)
self.reagents = self.reconcile_map(reagent_list=reagent_list, map=map)
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, map) -> List[dict]:
def reconcile_map(self, reagent_list, reagent_map) -> List[dict]:
output = []
for reagent in reagent_list:
try:
mp_info = map[reagent['role']]
mp_info = reagent_map[reagent['role']]
except KeyError:
continue
placeholder = copy(reagent)
@@ -182,7 +183,7 @@ class SampleWriter(object):
submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type
self.xl = xl
self.map = submission_type.construct_sample_map()['lookup_table']
self.sample_map = submission_type.construct_sample_map()['lookup_table']
self.samples = self.reconcile_map(sample_list)
def reconcile_map(self, sample_list: list):
@@ -200,10 +201,10 @@ class SampleWriter(object):
return sorted(output, key=lambda k: k['submission_rank'])
def write_samples(self):
sheet = self.xl[self.map['sheet']]
columns = self.map['sample_columns']
sheet = self.xl[self.sample_map['sheet']]
columns = self.sample_map['sample_columns']
for ii, sample in enumerate(self.samples):
row = self.map['start_row'] + (sample['submission_rank'] - 1)
row = self.sample_map['start_row'] + (sample['submission_rank'] - 1)
for k, v in sample.items():
try:
column = columns[k]
@@ -220,13 +221,15 @@ class EquipmentWriter(object):
submission_type = SubmissionType.query(name=submission_type)
self.submission_type = submission_type
self.xl = xl
map = self.submission_type.construct_equipment_map()
self.equipment = self.reconcile_map(equipment_list=equipment_list, map=map)
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, map: list):
def reconcile_map(self, equipment_list: list, equipment_map: list):
output = []
if equipment_list is None:
return output
for ii, equipment in enumerate(equipment_list, start=1):
mp_info = map[equipment['role']]
mp_info = equipment_map[equipment['role']]
# logger.debug(f"{equipment['role']} map: {mp_info}")
placeholder = copy(equipment)
if mp_info == {}: