pychemstation.utils.sequence_types

 1from __future__ import annotations
 2
 3import os.path
 4from enum import Enum
 5from typing import Optional, List
 6from dataclasses import dataclass, field
 7from pychemstation.utils.tray_types import Tray
 8
 9
10@dataclass
11class SequenceDataFiles:
12    """Class to represent files generated during a sequence.
13
14    :param sequence_name: the name of the sequence that is running
15    :param dir: the complete path of the directory generated for the sequence
16    :param child_dirs: the complete path of the files for sequence runs, contains the Chemstation data, `dir` and the sample run file.
17    """
18
19    sequence_name: str
20    dir: str
21    child_dirs: List[str] = field(default_factory=list)
22
23
24class SampleType(Enum):
25    SAMPLE = 1
26    BLANK = 2
27    CALIBRATION = 3
28    CONTROL = 4
29
30    @classmethod
31    def _missing_(cls, value):
32        return cls.SAMPLE
33
34
35class InjectionSource(Enum):
36    AS_METHOD = "As Method"
37    MANUAL = "Manual"
38    MSD = "MSD"
39    HIP_ALS = "HipAls"
40
41    @classmethod
42    def _missing_(cls, value):
43        return cls.HIP_ALS
44
45
46@dataclass
47class SequenceEntry:
48    """Class to represent each row of a sequence file, maps one to one to Chemstation."""
49
50    data_file: str
51    vial_location: Tray
52    sample_name: Optional[str] = None
53    method: Optional[str] = None
54    num_inj: Optional[int] = 1
55    inj_vol: Optional[float] = 2
56    inj_source: Optional[InjectionSource] = InjectionSource.HIP_ALS
57    sample_type: Optional[SampleType] = SampleType.SAMPLE
58
59
60@dataclass
61class SequenceTable:
62    """Class to represent a sequence file.
63
64    :param name: name of the sequence
65    :param rows: the entries
66    """
67
68    name: str
69    rows: list[SequenceEntry]
70
71    def __eq__(self, other) -> bool:
72        if not isinstance(other, SequenceTable):
73            return False
74
75        equal = True
76        for self_row, other_row in zip(self.rows, other.rows):
77            equal &= self_row.vial_location == other_row.vial_location
78            equal &= self_row.data_file == other_row.data_file
79            if self_row.method and other_row.method:
80                equal &= (
81                    os.path.split(os.path.normpath(self_row.method))[-1]
82                    == os.path.split(os.path.normpath(other_row.method))[-1]
83                )
84            equal &= self_row.num_inj == other_row.num_inj
85            equal &= self_row.inj_vol == other_row.inj_vol
86            equal &= self_row.inj_source == other_row.inj_source
87            equal &= self_row.sample_name == other_row.sample_name
88            equal &= self_row.sample_type == other_row.sample_type
89        return equal