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DAOTHER-9425: Prevent 'nm-pea-any' occasionally matches with 'nm-res-…
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…cya'
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@yokochi47
yokochi47 committed May 22, 2024
1 parent ac0d0f3 commit 7233727
Showing 1 changed file with 37 additions and 29 deletions.
66 changes: 37 additions & 29 deletions wwpdb/utils/nmr/NmrDpUtility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,7 @@
# 15-Dec-2022 M. Yokochi - merge CS and MR as a single NMR data file in CIF format with comprehensive molecular assembly information (DAOTHER-7407, NMR restraint remediation)
# 13-Jan-2023 M. Yokochi - add support for small angle X-ray scattering restraints (NMR restraint remediation)
# 24-Jan-2023 M. Yokochi - add support for heteronuclear relaxation data (NOE, T1, T2, T1rho, Order parameter) (NMR restraint remediation)
# 23-Feb-2023 M. Yokochi - combine spectral peak lists in any format into single NMR-STAR until Phase 2 release (DAOTHER-7407)
# 23-Feb-2023 M. Yokochi - combine spectral peak lists in any plain text format into single NMR-STAR until Phase 2 release (DAOTHER-7407)
# 24-Mar-2023 M. Yokochi - add 'nmr-nef2cif-deposit' and 'nmr-str2cif-deposit' workflow operations (DAOTHER-7407)
# 22-Jun-2023 M. Yokochi - convert model file when pdbx_poly_seq category is missing for reuploading nmr_data after unlock (DAOTHER-8580)
# 19-Jul-2023 M. Yokochi - fix not to merge restraint id (_Gen_dist_constraint.ID) if lower and upper bounds are different (DAOTHER-8705)
Expand All @@ -188,7 +188,7 @@
# 07-Mar-2024 M. Yokochi - extract pdbx_poly_seq_scheme.auth_mon_id as alt_cmop_id to prevent sequence mismatch due to 5-letter CCD ID (DAOTHER-9158 vs D_1300043061)
# 22-Mar-2024 M. Yokochi - test tautomeric states of histidine-like residue across models (DAOTHER-9252)
# 01-May-2024 M. Yokochi - merge cs/mr sequence extensions containing unknown residues (e.g UNK, DN, N) if necessary (NMR restraint remediation, 6fw4)
# 21-May-2024 M. Yokochi - block deposition using a peak list file in any binary format (DAOTHER-9425)
# 22-May-2024 M. Yokochi - block deposition using a peak list file in any binary format and prevent 'nm-pea-any' occasionally matches with 'nm-res-cya' (DAOTHER-9425)
##
""" Wrapper class for NMR data processing.
@author: Masashi Yokochi
Expand Down Expand Up @@ -1131,7 +1131,7 @@ def __init__(self, verbose=False, log=sys.stderr):
self.__release_mode = False
# whether to allow to raise internal error
self.__internal_mode = False
# whether to combine spectral peak list in any format into single NMR-STAR file (must be trued off after Phase 2, DAOTHER-7407)
# whether to combine spectral peak list in any plain text format into single NMR-STAR file (must be trued off after Phase 2, DAOTHER-7407)
self.__merge_any_pk_as_is = False

# whether to allow empty coordinate file path
Expand Down Expand Up @@ -11329,7 +11329,23 @@ def __detectContentSubTypeOfLegacyPk(self):
if file_name != original_file_name and original_file_name is not None:
file_name = f"{original_file_name} ({file_name})"

if is_binary_file(file_path):
has_spectral_peak = False

try:

with open(file_path, 'r', encoding='utf-8') as ifh:
has_header = False
for idx, line in enumerate(ifh):
if line.isspace() or comment_pattern.match(line):
if line.startswith('#INAME'):
has_header = True
continue
if is_peak_list(line, has_header):
has_spectral_peak = True
if has_spectral_peak or idx >= self.mr_max_spacer_lines:
break

except UnicodeDecodeError: # catch exception due to binary format (DAOTHER-9425)

err = f"The spectal peak list file {file_name!r} is not plain text file."

Expand All @@ -11342,20 +11358,6 @@ def __detectContentSubTypeOfLegacyPk(self):

continue

has_spectral_peak = False

with open(file_path, 'r', encoding='utf-8') as ifh:
has_header = False
for idx, line in enumerate(ifh):
if line.isspace() or comment_pattern.match(line):
if line.startswith('#INAME'):
has_header = True
continue
if is_peak_list(line, has_header):
has_spectral_peak = True
if has_spectral_peak or idx >= self.mr_max_spacer_lines:
break

if has_spectral_peak:
continue

Expand Down Expand Up @@ -11432,7 +11434,7 @@ def __detectContentSubTypeOfLegacyPk(self):
has_str_format = has_cif_format = False

if has_pdb_format:
err = f"The spectral peak list file {file_name!r} (any format) is identified as coordinate file. "\
err = f"The spectral peak list file {file_name!r} (any plain text format) is identified as coordinate file. "\
"Did you accidentally select the wrong format? Please re-upload the spectral peak list file."

self.report.error.appendDescription('content_mismatch',
Expand All @@ -11445,7 +11447,7 @@ def __detectContentSubTypeOfLegacyPk(self):
continue

if has_mr_header:
err = f"The spectral peak list file {file_name!r} (any format) is identified as {getRestraintFormatName('nm-res-mr')}. "\
err = f"The spectral peak list file {file_name!r} (any plain text format) is identified as {getRestraintFormatName('nm-res-mr')}. "\
"Did you accidentally select the wrong format? Please re-upload the spectral peak list file."

self.report.error.appendDescription('content_mismatch',
Expand Down Expand Up @@ -11492,7 +11494,7 @@ def __detectContentSubTypeOfLegacyPk(self):
mr_str = True

if cs_str:
err = f"The spectral peak list file {file_name!r} (any format) is identified as "\
err = f"The spectral peak list file {file_name!r} (any plain text format) is identified as "\
f"{self.readable_file_type[message['file_type']]} formatted assigned chemical shift file. "\
"Did you accidentally select the wrong format? Please re-upload the spectral peak list file."

Expand All @@ -11506,7 +11508,7 @@ def __detectContentSubTypeOfLegacyPk(self):
continue

if mr_str:
err = f"The spectral peak list file {file_name!r} (any format) is identified as "\
err = f"The spectral peak list file {file_name!r} (any plain text format) is identified as "\
f"{self.readable_file_type[message['file_type']]} formatted restraint file. "\
"Did you accidentally select the wrong format? Please re-upload the spectral peak list file."

Expand Down Expand Up @@ -11539,7 +11541,7 @@ def __detectContentSubTypeOfLegacyPk(self):

if len_possible_types == 0:

err = f"The spectral peak list file {file_name!r} (any format) is identified as {getRestraintFormatNames(valid_types)} file. "\
err = f"The spectral peak list file {file_name!r} (any plain text format) is identified as {getRestraintFormatNames(valid_types)} file. "\
"Did you accidentally select the wrong format? Please re-upload the spectral peak list file."

self.report.error.appendDescription('content_mismatch',
Expand All @@ -11551,7 +11553,7 @@ def __detectContentSubTypeOfLegacyPk(self):

elif len_valid_types == 0:

err = f"The spectral peak list file {file_name!r} (any format) can be {possible_types}. "\
err = f"The spectral peak list file {file_name!r} (any plain text format) can be {possible_types}. "\
"Did you accidentally select the wrong format? Please re-upload the spectral peak list file."

self.report.error.appendDescription('content_mismatch',
Expand All @@ -11563,7 +11565,7 @@ def __detectContentSubTypeOfLegacyPk(self):

else:

err = f"The spectral peak list file {file_name!r} (any format) is identified as {getRestraintFormatNames(valid_types)} file"\
err = f"The spectral peak list file {file_name!r} (any plain text format) is identified as {getRestraintFormatNames(valid_types)} file"\
f"and can be {getRestraintFormatNames(possible_types)} file as well. "\
"Did you accidentally select the wrong format? Please re-upload the spectral peak list file."

Expand Down Expand Up @@ -13770,7 +13772,8 @@ def __detectOtherPossibleFormatAsErrorOfLegacyMr(self, file_path, file_name, fil
valid_types.update(_valid_types)
possible_types.update(_possible_types)

if (not is_valid or multiple_check) and file_type != 'nm-res-cya':
# prevent 'nm-pea-any' occasionally matches with 'nm-res-cya' (DAOTHER-9425)
if (not is_valid or multiple_check) and file_type not in ('nm-res-cya', 'nm-pea-any'):
_is_valid, _err, _genuine_type, _valid_types, _possible_types =\
self.__detectOtherPossibleFormatAsErrorOfLegacyMr__(file_path, file_name, file_type, dismiss_err_lines, 'nm-res-cya')

Expand Down Expand Up @@ -13920,7 +13923,7 @@ def __detectOtherPossibleFormatAsErrorOfLegacyMr__(self, file_path, file_name, f
has_parser_error = parser_err_listener is not None and parser_err_listener.getMessageList() is not None

if (has_lexer_error or has_parser_error) and sll_pred\
and _file_type in ('nm-res-xml', 'nm-res-cns', 'nm-res-cha'):
and _file_type in ('nm-res-xpl', 'nm-res-cns', 'nm-res-cha'):
sll_pred = False

reader.setSllPredMode(sll_pred)
Expand Down Expand Up @@ -31656,7 +31659,7 @@ def __mergeStrPk(self):
return True

def __mergeAnyPkAsIs(self):
""" Merge spectral peak list file(s) in any format (file type: nm-pea-any) into a single NMR-STAR file as is.
""" Merge spectral peak list file(s) in any plain text format (file type: nm-pea-any) into a single NMR-STAR file as is.
"""

if self.__combined_mode:
Expand Down Expand Up @@ -31696,7 +31699,12 @@ def __mergeAnyPkAsIs(self):

file_path = ar['file_name']

if is_binary_file(file_path):
try:

with open(file_path, 'r', encoding='utf-8') as ifh:
ifh.read()

except UnicodeDecodeError: # catch exception due to binary format (DAOTHER-9425)
continue

content_subtype = 'spectral_peak'
Expand Down

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