|
1
|
|
|
# -*- coding: utf-8 -*- |
|
2
|
|
|
|
|
3
|
|
|
from bika.lims import api |
|
4
|
|
|
from bika.lims.utils.analysisrequest import create_partition |
|
5
|
|
|
from senaite.core import logger |
|
6
|
|
|
from senaite.core.interfaces import IAfterCreateSampleHook |
|
7
|
|
|
from senaite.core.registry import get_registry_record |
|
8
|
|
|
from zope.interface import implementer |
|
9
|
|
|
|
|
10
|
|
|
# Registry key constants |
|
11
|
|
|
REGISTRY_KEY_COPY_PARTITIONS = "sample_add_form_copy_partitions" |
|
12
|
|
|
|
|
13
|
|
|
|
|
14
|
|
|
@implementer(IAfterCreateSampleHook) |
|
15
|
|
|
class AfterCreateSampleHook(object): |
|
16
|
|
|
"""Copy sample structure with partitions |
|
17
|
|
|
""" |
|
18
|
|
|
|
|
19
|
|
|
def __init__(self, sample, request): |
|
20
|
|
|
self.sample = sample |
|
21
|
|
|
self.request = request |
|
22
|
|
|
|
|
23
|
|
|
def update(self, sample, source=None): |
|
24
|
|
|
"""Update handler |
|
25
|
|
|
|
|
26
|
|
|
:param sample: The newly created sample |
|
27
|
|
|
:param source: The source sample to copy from (optional) |
|
28
|
|
|
""" |
|
29
|
|
|
# Return immediately if we do not have a source sample |
|
30
|
|
|
# or the registry settings is set to False |
|
31
|
|
|
if not source or not self.get_copy_partitions(): |
|
32
|
|
|
return |
|
33
|
|
|
|
|
34
|
|
|
# Check if the source sample has partitions |
|
35
|
|
|
if not self.has_partitions(source): |
|
36
|
|
|
return |
|
37
|
|
|
|
|
38
|
|
|
# Get the partition config from the source sample |
|
39
|
|
|
configs = self.get_partition_configurations(source) |
|
40
|
|
|
|
|
41
|
|
|
# Nothing to do if we have no configs |
|
42
|
|
|
if not configs: |
|
43
|
|
|
return |
|
44
|
|
|
|
|
45
|
|
|
# Create the partitions in the target sample |
|
46
|
|
|
self.create_partitions_from_config(sample, configs) |
|
47
|
|
|
|
|
48
|
|
|
def get_copy_partitions(self): |
|
49
|
|
|
"""Returns whether to copy the sample structure with partitions |
|
50
|
|
|
|
|
51
|
|
|
:return: Boolean indicating if partition copying is enabled |
|
52
|
|
|
""" |
|
53
|
|
|
record = get_registry_record(REGISTRY_KEY_COPY_PARTITIONS) |
|
54
|
|
|
return bool(record) |
|
55
|
|
|
|
|
56
|
|
|
def has_partitions(self, sample): |
|
57
|
|
|
"""Check if the sample has partitions |
|
58
|
|
|
|
|
59
|
|
|
:param source: The source sample object |
|
60
|
|
|
:return: True if valid, False otherwise |
|
61
|
|
|
""" |
|
62
|
|
|
if not sample: |
|
63
|
|
|
return False |
|
64
|
|
|
|
|
65
|
|
|
partitions = sample.getDescendantsUIDs() |
|
66
|
|
|
|
|
67
|
|
|
if not partitions: |
|
68
|
|
|
return False |
|
69
|
|
|
|
|
70
|
|
|
return True |
|
71
|
|
|
|
|
72
|
|
|
def get_partition_configurations(self, source): |
|
73
|
|
|
"""Extract partition configurations from the source sample |
|
74
|
|
|
|
|
75
|
|
|
Returns a list of dictionaries containing partition configuration: |
|
76
|
|
|
- analyses: list of analysis objects |
|
77
|
|
|
- sample_type: SampleType UID or None |
|
78
|
|
|
- container: Container UID or None |
|
79
|
|
|
- preservation: Preservation UID or None |
|
80
|
|
|
|
|
81
|
|
|
:param source: The source sample object |
|
82
|
|
|
:return: List of partition configuration dictionaries |
|
83
|
|
|
""" |
|
84
|
|
|
if not source: |
|
85
|
|
|
return [] |
|
86
|
|
|
|
|
87
|
|
|
# Get all partitions from the source |
|
88
|
|
|
partitions = source.getDescendants(all_descendants=False) |
|
89
|
|
|
if not partitions: |
|
90
|
|
|
return [] |
|
91
|
|
|
|
|
92
|
|
|
configurations = [] |
|
93
|
|
|
for partition in partitions: |
|
94
|
|
|
# Get analyses that belong to this partition |
|
95
|
|
|
analyses = partition.getAnalyses(full_objects=True) |
|
96
|
|
|
|
|
97
|
|
|
# Get partition-specific settings |
|
98
|
|
|
sample_type = partition.getSampleType() |
|
99
|
|
|
container = partition.getContainer() |
|
100
|
|
|
preservation = partition.getPreservation() |
|
101
|
|
|
internal_use = partition.getInternalUse() |
|
102
|
|
|
|
|
103
|
|
|
config = { |
|
104
|
|
|
"analyses": analyses, |
|
105
|
|
|
"sample_type": sample_type, |
|
106
|
|
|
"container": container, |
|
107
|
|
|
"preservation": preservation, |
|
108
|
|
|
"internal_use": internal_use, |
|
109
|
|
|
} |
|
110
|
|
|
configurations.append(config) |
|
111
|
|
|
|
|
112
|
|
|
return configurations |
|
113
|
|
|
|
|
114
|
|
|
def create_partitions_from_config(self, primary_sample, configurations): |
|
115
|
|
|
"""Create partitions for a sample based on configurations |
|
116
|
|
|
|
|
117
|
|
|
:param primary_sample: The primary sample object |
|
118
|
|
|
:param configurations: List of partition configuration dicts |
|
119
|
|
|
:return: List of created partition objects |
|
120
|
|
|
""" |
|
121
|
|
|
if not configurations: |
|
122
|
|
|
return [] |
|
123
|
|
|
|
|
124
|
|
|
created_partitions = [] |
|
125
|
|
|
for idx, config in enumerate(configurations): |
|
126
|
|
|
analyses = config.get("analyses", []) |
|
127
|
|
|
sample_type = config.get("sample_type") |
|
128
|
|
|
container = config.get("container") |
|
129
|
|
|
preservation = config.get("preservation") |
|
130
|
|
|
internal_use = config.get("internal_use") |
|
131
|
|
|
|
|
132
|
|
|
logger.debug( |
|
133
|
|
|
"Creating partition {} of {} for sample {}".format( |
|
134
|
|
|
idx + 1, len(configurations), api.get_id(primary_sample)) |
|
135
|
|
|
) |
|
136
|
|
|
|
|
137
|
|
|
# Create the partition |
|
138
|
|
|
partition = create_partition( |
|
139
|
|
|
analysis_request=primary_sample, |
|
140
|
|
|
request=self.request, |
|
141
|
|
|
analyses=analyses, |
|
142
|
|
|
sample_type=sample_type, |
|
143
|
|
|
container=container, |
|
144
|
|
|
preservation=preservation, |
|
145
|
|
|
internal_use=internal_use, |
|
146
|
|
|
) |
|
147
|
|
|
created_partitions.append(partition) |
|
148
|
|
|
|
|
149
|
|
|
return created_partitions |
|
150
|
|
|
|
senaite /
senaite.core
