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fixes #348: raise exception if plate names too long #349

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fixes #348: raise exception if plate names too long #349

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143 changes: 119 additions & 24 deletions scadnano/scadnano.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,9 @@
default_scadnano_file_extension = "sc"
"""Default filename extension when writing a scadnano file."""

excel_sheet_name_max_length = 31
# maximum length of an Excel sheet name, used to check if plate name exceeds this length

VStrands = dict[int, dict[str, Any]]


Expand Down Expand Up @@ -8104,6 +8107,7 @@ def write_idt_plate_excel_file(
use_default_plates: bool = True,
warn_using_default_plates: bool = True,
plate_type: PlateType = PlateType.wells96,
raise_exception_if_plate_name_long: bool = True,
export_non_modified_strand_version: bool = False,
) -> None:
"""
Expand Down Expand Up @@ -8161,12 +8165,29 @@ def write_idt_plate_excel_file(
if the `use_default_plates` parameter is ``True``.
Ignored if `use_default_plates` is ``False``, because in that case the wells are explicitly set
by the user, who is free to use coordinates for either plate type.
:param raise_exception_if_plate_name_long:
Excel will not allow a sheet name longer than 31 characters. If this parameter is True (the default), then
an exception is raised if any :data:`VendorFields.plate` field is longer than 31 characters for any strand.
Set this parameter to False to allow the program to automatically truncate any plate name longer than
31 characters.
If set to False and any plate name exceeds 31 characters, a warning is printed for any plate name that
is truncated, reminding the user to manually change the plate name on IDT's website.
Since plate names are chosen by this method (``plate1``, ``plate2``, ...) rather than by the user
when `use_default_plates` is ``True``, they can never be too long in that case, so setting this
parameter to False requires also setting `use_default_plates` to ``False``.
Two plates cannot share one sheet, so if two plate names are identical in their first
31 characters, an exception is raised regardless of the value of this parameter.
:param export_non_modified_strand_version:
For any :any:`Strand` with a :any:`Modification`, also export a version of the :any:`Strand`
without any modifications. The name for this :any:`Strand` is the original name with
'_nomods' appended to it.
"""

if (not raise_exception_if_plate_name_long) and use_default_plates:
raise ValueError(
"If raise_exception_if_plate_name_long is False then use_default_plates must also be False"
)

strands_to_export = self._idt_strands_to_export(
key=key,
warn_duplicate_name=warn_duplicate_name,
Expand All @@ -8180,7 +8201,12 @@ def write_idt_plate_excel_file(
raise ValueError(
"parameters use_default_plates and only_strands_with_vendor_fields cannot both be False"
)
self._write_plates_assuming_explicit_plates_in_each_strand(directory, filename, strands_to_export)
self._write_plates_assuming_explicit_plates_in_each_strand(
directory,
filename,
strands_to_export,
raise_exception_if_plate_name_long=raise_exception_if_plate_name_long,
)
else:
self._write_plates_default(
directory=directory,
Expand All @@ -8190,34 +8216,109 @@ def write_idt_plate_excel_file(
warn_using_default_plates=warn_using_default_plates,
)

@staticmethod
def _msg_plate_name_too_long(plate_name: str, err: bool) -> str:
msg_prefix = (
f'The plate name "{plate_name}" is longer than {excel_sheet_name_max_length} characters, '
f"which is the maximum allowed by Excel."
)
if err:
msg = (
msg_prefix
+ """
Please shorten the plate name in the VendorFields.plate field of the strands in this plate,
or set the parameter raise_exception_if_plate_name_long=False in the call to Design.write_idt_plate_excel_file.
"""
)
else:
msg = f"""\
WARNING: {msg_prefix}
The plate name will be truncated to {excel_sheet_name_max_length} characters in the Excel file:
"{plate_name[:excel_sheet_name_max_length]}"
Please manually change the plate name on IDT's website if you want to retain the original name
{plate_name}
"""
return msg

@staticmethod
def _msg_plate_names_share_sheet_name(plate_name1: str, plate_name2: str, sheet_name: str) -> str:
return f"""\
The plate names
"{plate_name1}"
"{plate_name2}"
would both be written to a sheet named
"{sheet_name}"
since Excel allows at most {excel_sheet_name_max_length} characters in a sheet name,
and two plates cannot share one sheet.
Please shorten the plate names in the VendorFields.plate field of the strands on these plates so that
they differ within their first {excel_sheet_name_max_length} characters.
Setting raise_exception_if_plate_name_long=False does not avoid this error.
"""

def _write_plates_assuming_explicit_plates_in_each_strand(
self, directory: str, filename: str | None, strands_to_export: list[Strand]
self,
directory: str,
filename: str | None,
strands_to_export: list[Strand],
raise_exception_if_plate_name_long: bool,
) -> None:
plates = list(
plate_names = list(
{
strand.vendor_fields.plate
for strand in strands_to_export
if strand.vendor_fields is not None
if strand.vendor_fields.plate is not None
}
)
if len(plates) == 0:
if len(plate_names) == 0:
raise ValueError(
"Cannot write a a plate file since no plate data exists in any Strands "
"in the design.\n"
"Set the option use_default_plates=True in "
"Design.write_idt_plate_excel_file\nif you don't want to enter plate "
"and well positions for each Strand you wish to write to the Excel file."
)
plates.sort()
plate_names.sort()

# Excel cannot handle a sheet name longer than excel_sheet_name_max_length, so each plate name is
# mapped to the name of the sheet it will be written to, which is the plate name itself unless it
# is too long and we were asked to truncate rather than raise. The plate name itself is still what
# identifies the strands on the plate, so the two must be kept separate.
sheet_name_of_plate: dict[str, str] = {}
plate_of_sheet_name: dict[str, str] = {}
truncated_plate_names: list[str] = []
for plate_name in plate_names:
if len(plate_name) <= excel_sheet_name_max_length:
sheet_name = plate_name
elif raise_exception_if_plate_name_long:
msg = self._msg_plate_name_too_long(plate_name, err=True)
raise ValueError(msg)
else:
sheet_name = plate_name[:excel_sheet_name_max_length]
truncated_plate_names.append(plate_name)

# Distinct plate names can collapse to the same sheet name once truncated, and two plates
# cannot share one sheet, so this is an error even though we were asked not to raise an
# exception for a long plate name.
if sheet_name in plate_of_sheet_name:
msg = self._msg_plate_names_share_sheet_name(plate_of_sheet_name[sheet_name], plate_name, sheet_name)
raise ValueError(msg)
plate_of_sheet_name[sheet_name] = plate_name
sheet_name_of_plate[plate_name] = sheet_name

# warn only once the names of all sheets are known to be usable, so that no warning is printed
# about a plate name that one of the exceptions above then rejects the whole file for
for plate_name in truncated_plate_names:
print(self._msg_plate_name_too_long(plate_name, err=False))

filename_plate, workbook = self._setup_excel_file(directory, filename)
for plate in plates:
worksheet = self._add_new_excel_plate_sheet(plate, workbook)
for plate_name in plate_names:
worksheet = self._add_new_excel_plate_sheet(sheet_name_of_plate[plate_name], workbook)

strands_in_plate = [
strand
for strand in strands_to_export
if strand.vendor_fields is not None and strand.vendor_fields.plate == plate
if strand.vendor_fields is not None and strand.vendor_fields.plate == plate_name
]

strands_in_plate.sort(key=lambda s: (int(s.vendor_fields.well[1:]), s.vendor_fields.well[0])) # type: ignore
Expand Down Expand Up @@ -8258,14 +8359,14 @@ def _write_plates_default(
directory: str,
filename: str | None,
strands: list[Strand],
plate_type: PlateType = PlateType.wells96,
warn_using_default_plates: bool = True,
plate_type: PlateType,
warn_using_default_plates: bool,
) -> None:
plate_coord = PlateCoordinate(plate_type=plate_type)
plate = 1
plate_idx = 1
excel_row = 1
filename_plate, workbook = self._setup_excel_file(directory, filename)
worksheet = self._add_new_excel_plate_sheet(f"plate{plate}", workbook)
worksheet = self._add_new_excel_plate_sheet(f"plate{plate_idx}", workbook)

num_strands_per_plate = plate_type.num_wells_per_plate()
num_plates_needed = len(strands) // num_strands_per_plate
Expand Down Expand Up @@ -8313,10 +8414,10 @@ def _write_plates_default(
else:
plate_coord.advance()

if plate != plate_coord.plate():
if plate_idx != plate_coord.plate():
workbook.save(filename_plate)
plate = plate_coord.plate()
worksheet = self._add_new_excel_plate_sheet(f"plate{plate}", workbook)
plate_idx = plate_coord.plate()
worksheet = self._add_new_excel_plate_sheet(f"plate{plate_idx}", workbook)
excel_row = 1
else:
excel_row += 1
Expand Down Expand Up @@ -8782,13 +8883,9 @@ def add_nick(self, helix: int, offset: int, forward: bool, new_color: bool = Tru

# 5' modification stays with the strand keeping the 5' end, 3' modification with the other,
# and each internal modification goes to whichever side of the nick its base is on
mods_int_before = {
idx: mod for idx, mod in strand.modifications_int.items() if idx < num_bases_before
}
mods_int_before = {idx: mod for idx, mod in strand.modifications_int.items() if idx < num_bases_before}
mods_int_after = {
idx - num_bases_before: mod
for idx, mod in strand.modifications_int.items()
if idx >= num_bases_before
idx - num_bases_before: mod for idx, mod in strand.modifications_int.items() if idx >= num_bases_before
}

# a name/label identifies a single strand, so it cannot be given to both new strands; it goes
Expand Down Expand Up @@ -8966,9 +9063,7 @@ def ligate(self, helix: int, offset: int, forward: bool) -> None:
# the last num_bases_rotated bases (those of dom_3p) are now the first ones. The internal
# modification indices are rotated by the same amount to stay on the same bases.
if old_dna_sequence is not None:
strand.set_dna_sequence(
old_dna_sequence[-num_bases_rotated:] + old_dna_sequence[:-num_bases_rotated]
)
strand.set_dna_sequence(old_dna_sequence[-num_bases_rotated:] + old_dna_sequence[:-num_bases_rotated])
dna_length = strand.dna_length()
strand.modifications_int = {
(idx + num_bases_rotated) % dna_length: mod for idx, mod in strand.modifications_int.items()
Expand Down
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