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Start of custom context menu for procedure creation

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This commit is contained in:
lwark
2025-05-29 14:13:16 -05:00
parent fef964fba0
commit a2e1c52f22
6 changed files with 179 additions and 58 deletions
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11
src/submissions/backend/db/models/submissions.py
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@@ -1297,7 +1297,7 @@ class Run(BaseClass, LogMixin):
submission_rank = self.get_submission_rank_of_sample(sample=sample)
if submission_rank != 0:
row, column = plate_dict[submission_rank]
ranked_samples.append(dict(sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank, background_color="#6ffe1d"))
ranked_samples.append(dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank, background_color="#6ffe1d"))
else:
unranked_samples.append(sample)
possible_ranks = (item for item in list(plate_dict.keys()) if item not in [sample['submission_rank'] for sample in ranked_samples])
@@ -1310,21 +1310,18 @@ class Run(BaseClass, LogMixin):
continue
row, column = plate_dict[submission_rank]
ranked_samples.append(
dict(sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank,
dict(well_id=sample.sample_id, sample_id=sample.sample_id, row=row, column=column, submission_rank=submission_rank,
background_color="#6ffe1d"))
padded_list = []
for iii in range(1, proceduretype.total_wells+1):
sample = next((item for item in ranked_samples if item['submission_rank']==iii),
dict(sample_id="", row=0, column=0, submission_rank=iii)
dict(well_id=f"blank_{iii}", sample_id="", row=0, column=0, submission_rank=iii, background_color="#ffffff")
)
padded_list.append(sample)
logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
# logger.debug(f"Final padded list:\n{pformat(list(sorted(padded_list, key=itemgetter('submission_rank'))))}")
return list(sorted(padded_list, key=itemgetter('submission_rank')))
class SampleType(BaseClass):
id = Column(INTEGER, primary_key=True) #: primary key
name = Column(String(64), nullable=False, unique=True) #: identification from submitter

58
src/submissions/backend/validators/pydant.py
View File

@@ -1397,53 +1397,17 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
self.reagentrole = {}
self.possible_kits.insert(0, self.possible_kits.pop(self.possible_kits.index(kittype)))
def shuffle_samples(self, source_row: int, source_column: int, destination_row: int, destination_column=int):
logger.debug(f"Attempting sample shuffle.")
try:
source_sample = next(
(sample for sample in self.samples if sample.row == source_row and sample.column == source_column))
except StopIteration:
raise StopIteration("Couldn't find proper sample.")
logger.debug(f"Source Well: {source_row}, {source_column}")
logger.debug(f"Destination Well: {destination_row}, {destination_column}")
updateable_samples = []
if source_row > destination_row and source_column >= destination_column:
logger.debug(f"Sample was moved ahead.")
movement = "pos"
for sample in self.samples:
if sample.row >= destination_row and sample.column >= destination_column:
if sample.row <= source_row and sample.column <= source_column:
updateable_samples.append(sample)
elif source_row < destination_row and source_column <= destination_column:
logger.debug(f"Sample was moved back.")
movement = "neg"
for sample in self.samples:
if sample.row <= destination_row and sample.column <= destination_column:
if sample.row >= source_row and sample.column >= source_column:
updateable_samples.append(sample)
else:
logger.debug(f"Don't know what happened.")
logger.debug(f"Samples to be updated: {pformat(updateable_samples)}")
for sample in updateable_samples:
if sample.row == source_row and sample.column == source_column:
sample.row = destination_row
sample.column = destination_column
else:
match movement:
case "pos":
if sample.row + 1 > 8:
sample.column += 1
sample.row = 1
else:
sample.row += 1
case "neg":
if sample.row - 1 <= 0:
sample.column -= 1
sample.row = 8
else:
sample.row -= 1
def update_samples(self, sample_list: List[dict]):
logger.debug(f"Incoming sample_list:\n{pformat(sample_list)}")
for sample_dict in sample_list:
try:
sample = next((item for item in self.samples if item.sample_id.upper()==sample_dict['sample_id'].upper()))
except StopIteration:
continue
row, column = self.proceduretype.ranked_plate[sample_dict['index']]
sample.row = row
sample.column = column
logger.debug(f"Updated samples:\n{pformat(self.samples)}")
class PydClientSubmission(PydBaseClass):