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Use new sample sheet validation

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This commit is contained in:
Natalia Garcia 2026-05-22 12:58:17 +00:00
parent 1b3155d591
commit 2cfc7b2549
2 changed files with 36 additions and 54 deletions
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14
bin/workflow_glue/wfg_helpers/check_sample_sheet.py
View File

@ -39,12 +39,12 @@ def determine_codec(f):
return None # will cause file to be opened with default encoding
def load_validators(modules, wf_params):
def load_validators(modules, wf_params, options=None):
"""Load validator classes."""
validator_classes = []
for mod in modules:
for _, validator_class in getmembers(mod, _is_sample_sheet_validator):
validator_classes.append(validator_class(wf_params))
validator_classes.append(validator_class(wf_params, options))
return validator_classes
@ -76,11 +76,11 @@ def main(args):
if args.required_sample_types:
wf_params['required_sample_types'] = args.required_sample_types
# `no_barcode` is currently passed as a CLI option,
# not through the workflow params JSON.
wf_params['no_barcode'] = args.no_barcode
validator_classes = load_validators(load_validator_modules(), wf_params)
validator_classes = load_validators(
load_validator_modules(), wf_params, options={
"no_barcode": args.no_barcode,
}
)
rows = []

76
bin/workflow_glue/wfg_helpers/validators/default.py
View File

@ -11,9 +11,11 @@ import re
class SampleSheetValidator(ABC):
"""Base class for sample sheet validators."""
def __init__(self, wf_params):
def __init__(self, wf_params, options=None):
"""Initialize the validator with workflow parameters."""
self.wf_params = wf_params
self.options = options or {}
self.alias_field = "sample_name" if self.options.get("no_barcode") else "alias"
self.errors = []
def log_error(self, msg, column=None, lineno=None):
@ -46,13 +48,13 @@ class SampleSheetValidator(ABC):
class ProhibitedColumns(SampleSheetValidator):
"""Check for prohibited columns."""
def __init__(self, wf_params):
def __init__(self, wf_params, options=None):
"""Initialize with workflow parameters."""
super().__init__(wf_params)
super().__init__(wf_params, options)
def on_header(self, header):
"""Don't allow `barcode` and `alias` when `--no_barcode` set."""
if self.wf_params.get("no_barcode"):
if self.options.get("no_barcode"):
for field in ["alias", "barcode"]:
if field in header:
self.log_error(
@ -68,9 +70,10 @@ class RequiredColumns(SampleSheetValidator):
"""Check for required columns."""
self.header = header
required = ["barcode", "alias"]
if self.wf_params.get("no_barcode"):
required = ['sample_name']
required = [self.alias_field]
if not self.options.get("no_barcode"):
# in barcode mode required are alias_field and barcode
required.insert(0, "barcode")
for req in required:
if req not in header:
@ -89,9 +92,9 @@ class SampleTypeRules(SampleSheetValidator):
"test_sample", "positive_control", "negative_control", "no_template_control"
}
def __init__(self, wf_params):
def __init__(self, wf_params, options=None):
"""Initialize with workflow parameters."""
super().__init__(wf_params)
super().__init__(wf_params, options)
self.types = []
self.unexpected_types = []
self.required = wf_params.get("required_sample_types", [])
@ -123,38 +126,18 @@ class SampleTypeRules(SampleSheetValidator):
return valid
class NonEmptySampleSheet(SampleSheetValidator):
"""Check that the sample sheet has at least one data row."""
def __init__(self, wf_params):
"""Initialize with workflow parameters."""
super().__init__(wf_params)
self.row_count = 0
def add_sheet_row(self, row, lineno):
"""Count sample rows."""
self.row_count += 1
@property
def is_valid(self):
"""Check the sample sheet has at least one data row."""
if self.row_count == 0 and not self.errors:
self.log_error("Sample sheet must contain at least one data row")
return super().is_valid
class BarcodeRules(SampleSheetValidator):
"""Check barcode rules."""
def __init__(self, wf_params):
def __init__(self, wf_params, options=None):
"""Initialize with workflow parameters."""
super().__init__(wf_params)
super().__init__(wf_params, options)
self.first_len = None
self.barcodes = []
def add_sheet_row(self, row, lineno):
"""Check barcode rules."""
if self.wf_params.get("no_barcode"):
if self.options.get("no_barcode"):
return
bc = row.get("barcode")
@ -185,45 +168,44 @@ class BarcodeRules(SampleSheetValidator):
class AliasRules(SampleSheetValidator):
"""Alias rules."""
ALIAS_PATTERN = re.compile(r"^[A-Za-z0-9._-]+$")
ALIAS_PATTERN = re.compile(r"^[A-Za-z0-9][A-Za-z0-9._-]*$")
def __init__(self, wf_params):
def __init__(self, wf_params, options=None):
"""Initialize with workflow parameters."""
super().__init__(wf_params)
super().__init__(wf_params, options)
self.aliases = set()
def add_sheet_row(self, row, lineno):
"""Check alias rules."""
if self.wf_params.get("no_barcode"):
return
alias = row.get("alias")
alias = row.get(self.alias_field)
if alias is None:
self.log_error("Column missing", column="alias")
self.log_error("Column missing", column=self.alias_field)
return
if alias in self.aliases:
self.log_error(
f"Value not unique: {alias}", column="alias", lineno=lineno
f"Value not unique: {alias}", column=self.alias_field, lineno=lineno,
)
self.aliases.add(alias)
# Specific error message if empty "" to improve user error message
if not alias:
self.log_error(
f"Empty value: {alias}. Allowed values start with letters or numbers "
f"Empty {self.alias_field}. "
"Allowed values start with letters or numbers "
"and may contain only letters, numbers, '.', '_' or '-'",
column="alias",
column=self.alias_field,
lineno=lineno,
)
if not self.ALIAS_PATTERN.match(alias):
self.log_error(
f"Invalid value {alias}. Allowed values start with letters or numbers "
"and may contain only letters, numbers, '.', '_' or '-'",
column="alias",
column=self.alias_field,
lineno=lineno,
)
if alias.startswith("barcode"):
self.log_error(
f"Value must not begin with 'barcode': {alias}",
column="alias",
column=self.alias_field,
lineno=lineno,
)
@ -231,9 +213,9 @@ class AliasRules(SampleSheetValidator):
class AnalysisGroupCompleteness(SampleSheetValidator):
"""Analysis groups."""
def __init__(self, wf_params):
def __init__(self, wf_params, options=None):
"""Initialize with workflow parameters."""
super().__init__(wf_params)
super().__init__(wf_params, options)
self.has_analysis_groups = False
def on_header(self, header):