mh_utils.worklist_parser

Parser for MassHunter worklists.

Only one function is defined here: read_worklist(), which reads the reads the given worklist file and returns a mh_utils.worklist_parser.classes.Worklist file representing it. The other functions and classes must be imported from submodules of this package.

read_worklist(filename)

Read the worklist from the given file.

Parameters

filename (Union[str, Path, PathLike]) – The filename of the worklist.

Return type

Worklist

Submodules

• mh_utils.worklist_parser.classes
  • Attribute
  • Checksum
  • JobData
  • Macro
  • Worklist
• mh_utils.worklist_parser.columns
  • Column
  • injection_volume
  • columns
• mh_utils.worklist_parser.enums
  • AttributeType
• mh_utils.worklist_parser.parser
  • parse_datetime
  • parse_params
  • parse_sample_info
  • sample_info_tags

Example Usage

read_worklist.py  worklist.wkl

read_worklist.py

# 3rd party
from pandas import DataFrame

# this package
from mh_utils.worklist_parser import Worklist, read_worklist

# Replace 'worklist.wkl' with the filename of your worklist.
wkl: Worklist = read_worklist("worklist.wkl")

df: DataFrame = wkl.as_dataframe()

# Filter columns
df = df[["Sample Name", "Method", "Data File", "Drying Gas", "Gas Temp", "Nebulizer"]]

# Get just the filename from 'Method' and 'Data File'
df["Method"] = [x.name for x in df["Method"]]
df["Data File"] = [x.name for x in df["Data File"]]

# Show the DataFrame
print(df.to_string())

worklist_df_head.txt

                   Sample Name                                   Method                                      Data File   Drying Gas   Gas Temp   Nebulizer
0           Methanol Blank +ve        Maitre Gunshot Residue Positive.m          Methanol_Blank_+ve_191121-0001-r001.d
1           Propellant 1mg +ve        Maitre Gunshot Residue Positive.m          Propellant_1mg_+ve_191121-0002-r001.d
2           Propellant 1ug +ve        Maitre Gunshot Residue Positive.m          Propellant_1ug_+ve_191121-0003-r001.d
3           Methanol Blank -ve        Maitre Gunshot Residue Negative.m          Methanol_Blank_-ve_191121-0004-r001.d
4           Propellant 1mg -ve        Maitre Gunshot Residue Negative.m          Propellant_1mg_-ve_191121-0005-r001.d
5           Propellant 1ug -ve        Maitre Gunshot Residue Negative.m          Propellant_1ug_-ve_191121-0006-r001.d
6       Methanol Blank +ve 5ul    Maitre Gunshot Residue Positive 5ul.m      Methanol_Blank_+ve_5ul_191121-0007-r001.d
7       Propellant 1mg +ve 5ul    Maitre Gunshot Residue Positive 5ul.m      Propellant_1mg_+ve_5ul_191121-0008-r001.d
8       Propellant 1ug +ve 5ul    Maitre Gunshot Residue Positive 5ul.m      Propellant_1ug_+ve_5ul_191121-0009-r001.d
9               Methanol Blank    Maitre Gunshot Residue Positive 5ul.m              Methanol_Blank_191121-0010-r001.d
10      Propellant 1mg gas 200    Maitre Gunshot Residue Positive 5ul.m      Propellant_1mg_gas_200_191121-0011-r001.d                   200
11      Propellant 1ug gas 200    Maitre Gunshot Residue Positive 5ul.m      Propellant_1ug_gas_200_191121-0012-r001.d                   200
12      Propellant 1mg gas 280    Maitre Gunshot Residue Positive 5ul.m      Propellant_1mg_gas_280_191121-0013-r001.d                   280
13      Propellant 1ug gas 280    Maitre Gunshot Residue Positive 5ul.m      Propellant_1ug_gas_280_191121-0014-r001.d                   280
14    Propellant 1mg drying 14    Maitre Gunshot Residue Positive 5ul.m    Propellant_1mg_drying_14_191121-0015-r001.d           14
15    Propellant 1ug drying 14    Maitre Gunshot Residue Positive 5ul.m    Propellant_1ug_drying_14_191121-0016-r001.d           14
16    Propellant 1mg drying 16    Maitre Gunshot Residue Positive 5ul.m    Propellant_1mg_drying_16_191121-0017-r001.d           16
17    Propellant 1ug drying 16    Maitre Gunshot Residue Positive 5ul.m    Propellant_1ug_drying_16_191121-0018-r001.d           16
18    Propellant 1mg drying 18    Maitre Gunshot Residue Positive 5ul.m    Propellant_1mg_drying_18_191121-0019-r001.d           18
19    Propellant 1ug drying 18    Maitre Gunshot Residue Positive 5ul.m    Propellant_1ug_drying_18_191121-0020-r001.d           18
20     Propellant 1mg nebul 40    Maitre Gunshot Residue Positive 5ul.m     Propellant_1mg_nebul_40_191121-0021-r001.d                                40
21     Propellant 1ug nebul 40    Maitre Gunshot Residue Positive 5ul.m     Propellant_1ug_nebul_40_191121-0022-r001.d                                40
22     Propellant 1mg nebul 50    Maitre Gunshot Residue Positive 5ul.m     Propellant_1mg_nebul_50_191121-0023-r001.d                                50
23     Propellant 1ug nebul 50    Maitre Gunshot Residue Positive 5ul.m     Propellant_1ug_nebul_50_191121-0024-r001.d                                50
24     Propellant 1mg nebul 60    Maitre Gunshot Residue Positive 5ul.m     Propellant_1mg_nebul_60_191121-0025-r001.d                                60
25     Propellant 1ug nebul 60    Maitre Gunshot Residue Positive 5ul.m     Propellant_1ug_nebul_60_191121-0026-r001.d                                60
...

read_worklist.py

# save as CSV
df.to_csv("worklist.csv")

# save as JSON
df.to_json("worklist.json", indent=2)

Output

worklist.csv  worklist.json