Merge pull request #18 from moka-guys/v1.3.0

V1.3.0 (#18) Co-Authored-By: Graeme <[email protected]> Co-Authored-By: rebeccahaines1 <[email protected]>
moka-guys · Jun 21, 2024 · 381ddcb · 381ddcb
2 parents 872b630 + 694dabf
commit 381ddcb
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diff --git a/README.md b/README.md
@@ -19,7 +19,7 @@ Runs a series of checks on the sample sheet, collects any errors identified. Che
 * Pan numbers are in the list of allowed pan numbers supplied to the script
 * Samplesheet contains any TSO samples
 
-If samplesheet contains an input dev_panno, the package will skip samplesheet chcks for the samplesheet.
+If samplesheet contains an input dev_pannos, the package will skip samplesheet checks for the samplesheet.
 
 ## Usage
 
@@ -40,7 +40,7 @@ sscheck_obj = SamplesheetCheck(
  sequencer_ids, # list
  panels, # list
  tso_panels, # list
- dev_panno, # str
+ dev_pannos, # list
  logdir, # str
 )
 sscheck_obj.ss_checks() # Carry out samplesheeet validation
@@ -73,8 +73,8 @@ options:
  Comma separated string of allowed panel numbers
  -T TSO_PANELS, --tso_panels TSO_PANELS
  Comma separated string of tso panels
- -D DEV_PANNO, --dev_panno DEV_PANNO
- Development pan number
+ -D DEV_PANNOS, --dev_pannos DEV_PANNOS
+ Development pan numbers
  -L LOGDIR, --logdir LOGDIR
  Directory to save the output logfile to
  -NSH NO_STREAM_HANDLER, --no_stream_handler NO_STRAM_HANDLER

diff --git a/pytest.ini b/pytest.ini
@@ -1,2 +1,2 @@
 [pytest]
-addopts = -v --ignore=test/data/ --ignore=test/temp/ --cov=. --cov-report term-missing --sequencer_ids=NB551068,NB552085,M02353,M02631,A01229 --tso_panels=Pan4969,Pan5085,Pan5112,Pan5114 --dev_panno=Pan5180 --panels=Pan5180,Pan4009,Pan2835,Pan4940,Pan4396,Pan5113,Pan5115,Pan4969,Pan5085,Pan5112,Pan5114,Pan5007,Pan5008,Pan5009,Pan5010,Pan5011,Pan5012,Pan5013,Pan5014,Pan5015,Pan5016,Pan4119,Pan4121,Pan4122,Pan4125,Pan4126,Pan4974,Pan4975,Pan4976,Pan4977,Pan4978,Pan4979,Pan4980,Pan4981,Pan4982,Pan4983,Pan4984,Pan4821,Pan4822,Pan4823,Pan4824,Pan4825,Pan4149,Pan4150,Pan4129,Pan4964,Pan4130,Pan5121,Pan5185,Pan5186,Pan5143,Pan5147,Pan4816,Pan4817,Pan5122,Pan5144,Pan5148,Pan4819,Pan4820,Pan4145,Pan4146,Pan4132,Pan4134,Pan4136,Pan4137,Pan4138,Pan4143,Pan4144,Pan4151,Pan4314,Pan4351,Pan4387,Pan4390,Pan4826,Pan4827,Pan4828,Pan4829,Pan4830,Pan4831,Pan4832,Pan4833,Pan4834,Pan4835,Pan4836 --logdir=.
+addopts = -v --ignore=test/data/ --ignore=test/temp/ --cov=. --cov-report term-missing --sequencer_ids=NB551068,NB552085,M02353,M02631,A01229 --tso_panels=Pan5085,Pan5112,Pan5114 --dev_pannos=Pan5180,Pan5227 --panels=Pan5180,Pan4009,Pan2835,Pan4940,Pan4396,Pan5113,Pan5115,Pan5226,Pan5085,Pan5112,Pan5114,Pan5007,Pan5008,Pan5009,Pan5010,Pan5011,Pan5012,Pan5013,Pan5014,Pan5015,Pan5016,Pan4119,Pan4121,Pan4122,Pan4125,Pan4126,Pan4974,Pan4975,Pan4976,Pan4977,Pan4978,Pan4979,Pan4980,Pan4981,Pan4982,Pan4983,Pan4984,Pan4821,Pan4822,Pan4823,Pan4824,Pan4825,Pan4149,Pan4150,Pan4129,Pan4964,Pan4130,Pan5121,Pan5185,Pan5186,Pan5143,Pan5147,Pan4816,Pan4817,Pan5122,Pan5144,Pan5148,Pan4819,Pan4820,Pan4145,Pan4146,Pan4132,Pan4134,Pan4136,Pan4137,Pan4138,Pan4143,Pan4144,Pan4151,Pan4314,Pan4351,Pan4387,Pan4390,Pan4826,Pan4827,Pan4828,Pan4829,Pan4830,Pan4831,Pan4832,Pan4833,Pan4834,Pan4835,Pan4836 --logdir=.
diff --git a/samplesheet_validator/__main__.py b/samplesheet_validator/__main__.py
@@ -50,10 +50,10 @@ def get_arguments():
  )
  parser.add_argument(
  "-D",
- "--dev_panno",
+ "--dev_pannos",
  type=str,
  required=True,
- help="Development pan number",
+ help="Comma separated string of development pan numbers",
  )
  parser.add_argument(
  "-L",
@@ -65,7 +65,7 @@ def get_arguments():
  parser.add_argument(
  "-NSH",
  "--no_stream_handler",
- action='store_true',
+ action="store_true",
  required=False,
  help=(
  "Provide flag when we don't want a stream handler (prevents duplication of log messages "
@@ -101,7 +101,6 @@ def is_valid_dir(parser: argparse.ArgumentParser, dir: str) -> str:
  return dir
 
 
-
 if __name__ == "__main__":
  parsed_args = get_arguments()
  logger = set_root_logger(parsed_args.no_stream_handler)
@@ -110,8 +109,7 @@ def is_valid_dir(parser: argparse.ArgumentParser, dir: str) -> str:
  parsed_args.sequencer_ids,
  parsed_args.panels,
  parsed_args.tso_panels,
- parsed_args.dev_panno,
+ parsed_args.dev_pannos,
  parsed_args.logdir,
  )
  sscheck_obj.ss_checks() # Carry out samplesheeet validation
-
diff --git a/samplesheet_validator/git_tag.py b/samplesheet_validator/git_tag.py
@@ -11,8 +11,11 @@ def git_tag() -> str:
  cmd = f"git -C {filepath} describe --tags"
 
  proc = subprocess.Popen(
- [cmd], stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True,
+ [cmd],
+ stderr=subprocess.PIPE,
+ stdout=subprocess.PIPE,
+ shell=True,
  )
  out, _ = proc.communicate()
  # Return standard out, removing any new line characters
- return out.rstrip().decode("utf-8")
+ return out.rstrip().decode("utf-8")
diff --git a/samplesheet_validator/samplesheet_validator.py b/samplesheet_validator/samplesheet_validator.py
@@ -14,7 +14,6 @@
 import re
 import logging
 from typing import Union
-from . import config
 from .ss_logger import SSLogger
 from seglh_naming.sample import Sample
 from seglh_naming.samplesheet import Samplesheet
@@ -45,7 +44,7 @@ class SamplesheetCheck:
  development_panels (list): Development pan numbers
  runfolder_name (str): Name of runfolder
  logfile_path (str): Path to use for logfile
- logger (logging.Logger): Logger 
+ logger (logging.Logger): Logger
 
  Methods:
  get_logger()
@@ -91,7 +90,7 @@ def __init__(
  sequencer_ids: list,
  panels: list,
  tso_panels: list,
- dev_panno: str,
+ dev_pannos: list,
  logdir: str,
  ):
  """
@@ -100,7 +99,7 @@ def __init__(
  :param sequencer_ids (list): Allowed sequencer IDs
  :param panels (list): Allowed pan numbers
  :param tso_panels (list): TSO500 pan numbers
- :param dev_panno (str):  Development pan number
+ :param dev_pannos (list): Development pan numbers
  :param logdir (str): Log file directory
  """
  self.samplesheet_path = samplesheet_path
@@ -118,20 +117,22 @@ def __init__(
  self.sequencer_ids = sequencer_ids
  self.panels = panels
  self.tso_panels = tso_panels
- self.dev_panno = dev_panno
- self.runfolder_name = (self.samplesheet_path.split("/")[-1]).split("_SampleSheet.csv")[0]
- self.logfile_path = f"{os.path.join(logdir, self.runfolder_name)}_samplesheet_validator.log"
+ self.dev_pannos = dev_pannos
+ self.runfolder_name = (self.samplesheet_path.split("/")[-1]).split(
+ "_SampleSheet.csv"
+ )[0]
+ self.logfile_path = (
+ f"{os.path.join(logdir, self.runfolder_name)}_samplesheet_validator.log"
+ )
  self.logger = self.get_logger()
 
-
  def get_logger(self) -> logging.Logger:
  """
  Get logger for the class
  :return (object): Logger
  """
  return SSLogger(self.logfile_path, self.runfolder_name).get_logger(__name__)
 
-
  def ss_checks(self) -> None:
  """
  Run checks at samplesheet and sample level. Performs required extra checks for
@@ -222,7 +223,11 @@ def development_run(self) -> Union[bool, None]:
  :return True | None: True if contains dev pan numbers, None if does not
  """
  strings_to_check = self.samples["Sample_ID"] + self.samples["Sample_Name"]
- if any(self.dev_panno in sample_name for sample_name in strings_to_check):
+
+ if any(
+ any(dev_panno in sample_string for sample_string in strings_to_check)
+ for dev_panno in self.dev_pannos
+ ):
  self.logger.info(
  self.logger.log_msgs["dev_run"],
  self.samplesheet_path,
@@ -286,7 +291,9 @@ def get_data_section(self) -> None:
  self.extract_headers(line, line_index)
  break
  elif len(line.split(",")[0]) < 2:
- self.logger.info(self.logger.log_msgs["found_empty_line"], line_index)
+ self.logger.info(
+ self.logger.log_msgs["found_empty_line"], line_index
+ )
  pass # Skip empty lines
  else: # Contains sample
  self.extract_sample_name_id(line, line_index)
@@ -307,7 +314,8 @@ def extract_headers(self, line: str, line_index: int) -> None:
  )
  self.add_msg_to_error_dict(
  "Error extracting headers",
- self.logger.log_msgs["error_extracting_headers"] % (line_index, exception),
+ self.logger.log_msgs["error_extracting_headers"]
+ % (line_index, exception),
  )
 
  def extract_sample_name_id(self, line: str, line_index: int) -> None:
@@ -324,11 +332,16 @@ def extract_sample_name_id(self, line: str, line_index: int) -> None:
  except Exception as exception:
  self.errors = True
  self.logger.warning(
- self.logger.log_msgs["col_extraction_error"], col_name, line_index, line, exception,
+ self.logger.log_msgs["col_extraction_error"],
+ col_name,
+ line_index,
+ line,
+ exception,
  )
  self.add_msg_to_error_dict(
  "Error extracting sample name and ID",
- self.logger.log_msgs["col_extraction_error"] % (col_name, line_index, line, exception)
+ self.logger.log_msgs["col_extraction_error"]
+ % (col_name, line_index, line, exception),
  )
 
  def check_expected_headers(self) -> None:
@@ -340,7 +353,9 @@ def check_expected_headers(self) -> None:
  if not all(
  header in self.data_headers for header in self.expected_data_headers
  ):
- self.missing_headers = list(set(self.expected_data_headers).difference(self.data_headers))
+ self.missing_headers = list(
+ set(self.expected_data_headers).difference(self.data_headers)
+ )
  self.errors = True
  self.add_msg_to_error_dict(
  "Missing headers",

diff --git a/samplesheet_validator/ss_logger.py b/samplesheet_validator/ss_logger.py
@@ -2,6 +2,7 @@
 
 Class used to create Samplesheet Validator logfiles
 """
+
 import sys
 from . import config
 import logging
@@ -30,7 +31,6 @@ def set_root_logger(no_stream_handler: bool):
  return logger
 
 
-
 class SSLogger:
  """
  Creates a python logging object with a file handler and syslog handler

diff --git a/settings.json b/settings.json
@@ -0,0 +1,37 @@
+{
+ "python.testing.pytestArgs": [
+ "."
+ ],
+ "python.testing.unittestEnabled": false,
+ "python.testing.pytestEnabled": true,
+ "python.envFile": "${workspaceFolder}/.venv",
+ "python.analysis.extraPaths": [
+ ],
+ "editor.formatOnSaveMode": "file",
+ "editor.formatOnSave": true,
+ "editor.codeActionsOnSave": {
+ "source.organizeImports": "explicit"
+ },
+ "[python]": {
+ "editor.defaultFormatter": "ms-python.black-formatter",
+ "editor.formatOnSave": true,
+ "editor.codeActionsOnSave": {
+ "source.organizeImports": "explicit"
+ }
+ },
+ "isort.args": [
+ "--profile",
+ "black"
+ ],
+ "flake8.args": [
+ "--max-line-length=120"
+ ],
+ "pylint.args": [
+ "--max-line-length=120"
+ ],
+ "black-formatter.args": [
+ "--line-length",
+ "120"
+ ],
+ "python.analysis.typeCheckingMode": "basic"
+}
diff --git a/setup.py b/setup.py
@@ -3,7 +3,7 @@
 
 setup(
  name="samplesheet_validator",
- version="TEST",
+ version=git_tag(),
  description="Python library for samplesheet validation",
  url="https://github.com/moka-guys/samplesheet_validator",
  author="Rachel Duffin",

diff --git a/test/conftest.py b/test/conftest.py
@@ -13,36 +13,11 @@
 
 
 def pytest_addoption(parser):
- parser.addoption(
- "--sequencer_ids",
- action="store",
- type=str,
- required=True,
- )
- parser.addoption(
- "--panels",
- action="store",
- type=str,
- required=True,
- )
- parser.addoption(
- "--tso_panels",
- action="store",
- type=str,
- required=True,
- )
- parser.addoption(
- "--dev_panno",
- action="store",
- type=str,
- required=True
- )
- parser.addoption(
- "--logdir",
- action="store",
- type=str,
- required=True,
- )
+ parser.addoption("--sequencer_ids", action="store", type=str, required=True)
+ parser.addoption("--panels", action="store", type=str, required=True)
+ parser.addoption("--tso_panels", action="store", type=str, required=True)
+ parser.addoption("--dev_pannos", action="store", type=str, required=True)
+ parser.addoption("--logdir", action="store", type=str, required=True)
 
 
 def pytest_configure(config):
@@ -52,7 +27,7 @@ def pytest_configure(config):
  os.environ["sequencer_ids"] = config.getoption("sequencer_ids")
  os.environ["panels"] = config.getoption("panels")
  os.environ["tso_panels"] = config.getoption("tso_panels")
- os.environ["dev_panno"] = config.getoption("dev_panno")
+ os.environ["dev_pannos"] = config.getoption("dev_pannos")
  data_dir = os.path.abspath("test/data/")
  os.environ["samplesheet_dir"] = f'{os.path.join(data_dir, "samplesheets")}'
  # Temporary directories to copy test files into and to contain outputs

diff --git a/test/data/samplesheets/valid/231012_M02631_0285_000000000-ERTFB_SampleSheet.csv b/test/data/samplesheets/valid/231012_M02631_0285_000000000-ERTFB_SampleSheet.csv
@@ -0,0 +1,27 @@
+[Header],,,,,,,,,
+IEMFileVersion,4,,,,,,,,
+Investigator Name,DEV01,,,,,,,,
+Experiment Name,DEV01,,,,,,,,
+Date,12/10/2023,,,,,,,,
+Workflow,GenerateFASTQ,,,,,,,,
+Application,FASTQ Only,,,,,,,,
+Assay,Nextera XT,,,,,,,,
+Description,DEV01,,,,,,,,
+Chemistry,Amplicon,,,,,,,,
+,,,,,,,,,
+[Reads],,,,,,,,,
+251,,,,,,,,,
+251,,,,,,,,,
+,,,,,,,,,
+[Settings],,,,,,,,,
+ReverseComplement,0,,,,,,,,
+Adapter,AGATCGGAAGAGCACACGTCTGAACTCCAGTCA,,,,,,,,
+AdapterRead2,AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT,,,,,,,,
+,,,,,,,,,
+[Data],,,,,,,,,
+Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description
+DEV01_01_000000_0000000_Pan5227,DEV01_01_000000_0000000_Pan5227,,,IDT8_UDI_1_2,CTGATCGT,IDT8_UDI_1_1,ATATGCGC,,
+DEV01_02_000000_0000000_Pan5227,DEV01_02_000000_0000000_Pan5227,,,IDT8_UDI_2_2,ACTCTCGA,IDT8_UDI_2_1,TGGTACAG,,
+DEV01_03_000000_NTC0000_Pan5227,DEV01_03_000000_NTC0000_Pan5227,,,IDT8_UDI_3_2,TGAGCTAG,IDT8_UDI_3_1,AACCGTTC,,
+DEV01_04_000000_0000000_Pan5227,DEV01_04_000000_0000000_Pan5227,,,IDT8_UDI_4_2,GAGACGAT,IDT8_UDI_4_1,TAACCGGT,,
+DEV01_05_000000_0000000_Pan5227,DEV01_05_000000_0000000_Pan5227,,,IDT8_UDI_5_2,CTTGTCGA,IDT8_UDI_5_1,GAACATCG,,
diff --git a/test/test_samplesheet_validator.py b/test/test_samplesheet_validator.py
@@ -10,6 +10,8 @@
 from samplesheet_validator.__main__ import is_valid_dir, is_valid_file
 
 
+# TODO add second dev pan number in
+
 def shutdown_logs(logger: object) -> None:
  """
  To prevent duplicate filehandlers and system handlers close
@@ -33,7 +35,7 @@ def get_sscheck_obj(samplesheet: str) -> object:
  os.getenv("sequencer_ids").split(","),
  os.getenv("panels").split(","),
  os.getenv("tso_panels").split(","),
- os.getenv("dev_panno"),
+ os.getenv("dev_pannos").split(","),
  os.getenv("temp_dir"),
  )
  sscheck_obj.ss_checks()
@@ -66,6 +68,11 @@ def valid_dev_samplesheet():
  os.getenv("samplesheet_dir"),
  "valid",
  "231012_M02631_0285_000000000-LBGMH_SampleSheet.csv",
+ ),
+ os.path.join(
+ os.getenv("samplesheet_dir"),
+ "valid",
+ "231012_M02631_0285_000000000-ERTFB_SampleSheet.csv",
  )
  ]