|
1
|
|
|
#!/usr/bin/env python3 |
|
2
|
|
|
# -*- coding: utf-8 -*- |
|
3
|
|
|
""" |
|
4
|
|
|
Created on Tue Feb 6 12:41:05 2018 |
|
5
|
|
|
|
|
6
|
|
|
@author: Paolo Cozzi <[email protected]> |
|
7
|
|
|
|
|
8
|
|
|
Common functions in uid |
|
9
|
|
|
|
|
10
|
|
|
""" |
|
11
|
|
|
|
|
12
|
|
|
import re |
|
13
|
|
|
import logging |
|
14
|
|
|
|
|
15
|
|
|
from language.helpers import check_species_synonyms |
|
16
|
|
|
|
|
17
|
|
|
from .models import Animal, Sample, DictSpecie |
|
18
|
|
|
|
|
19
|
|
|
# Get an instance of a logger |
|
20
|
|
|
logger = logging.getLogger(__name__) |
|
21
|
|
|
|
|
22
|
|
|
# a pattern to correctly parse aliases |
|
23
|
|
|
ALIAS_PATTERN = re.compile(r"IMAGE([AS])([0-9]+)") |
|
24
|
|
|
|
|
25
|
|
|
|
|
26
|
|
|
def parse_image_alias(alias): |
|
27
|
|
|
"""Parse alias and return table and pk""" |
|
28
|
|
|
|
|
29
|
|
|
match = re.search(ALIAS_PATTERN, alias) |
|
30
|
|
|
|
|
31
|
|
|
if not match: |
|
32
|
|
|
raise Exception("Cannot deal with '%s'" % (alias)) |
|
33
|
|
|
|
|
34
|
|
|
letter, padded_pk = match.groups() |
|
35
|
|
|
table, pk = None, None |
|
36
|
|
|
|
|
37
|
|
|
if letter == "A": |
|
38
|
|
|
table = "Animal" |
|
39
|
|
|
|
|
40
|
|
|
elif letter == "S": |
|
41
|
|
|
table = "Sample" |
|
42
|
|
|
|
|
43
|
|
|
pk = int(padded_pk) |
|
44
|
|
|
|
|
45
|
|
|
return table, pk |
|
46
|
|
|
|
|
47
|
|
|
|
|
48
|
|
|
def get_model_object(table, pk): |
|
49
|
|
|
"""Get a model object relying on table name (Sample/Alias) and pk""" |
|
50
|
|
|
|
|
51
|
|
|
# get sample object |
|
52
|
|
|
if table == "Animal": |
|
53
|
|
|
sample_obj = Animal.objects.get(pk=pk) |
|
54
|
|
|
|
|
55
|
|
|
elif table == "Sample": |
|
56
|
|
|
sample_obj = Sample.objects.get(pk=pk) |
|
57
|
|
|
|
|
58
|
|
|
else: |
|
59
|
|
|
raise Exception("Unknown table '%s'" % (table)) |
|
60
|
|
|
|
|
61
|
|
|
return sample_obj |
|
62
|
|
|
|
|
63
|
|
|
|
|
64
|
|
|
class FileDataSourceMixin(): |
|
65
|
|
|
"""A class to deal with common operation between Template and CRBanim |
|
66
|
|
|
files""" |
|
67
|
|
|
|
|
68
|
|
|
def check_items(self, item_set, model, column): |
|
69
|
|
|
"""General check of DataSource items into database""" |
|
70
|
|
|
|
|
71
|
|
|
# a list of not found terms and a status to see if something is missing |
|
72
|
|
|
# or not |
|
73
|
|
|
not_found = [] |
|
74
|
|
|
result = True |
|
75
|
|
|
|
|
76
|
|
|
for item in item_set: |
|
77
|
|
|
# check for species in database |
|
78
|
|
|
if not model.objects.filter(label=item).exists(): |
|
79
|
|
|
not_found.append(item) |
|
80
|
|
|
|
|
81
|
|
|
if len(not_found) != 0: |
|
82
|
|
|
result = False |
|
83
|
|
|
logger.warning( |
|
84
|
|
|
"Those %s are not present in UID database:" % (column)) |
|
85
|
|
|
logger.warning(not_found) |
|
86
|
|
|
|
|
87
|
|
|
return result, not_found |
|
88
|
|
|
|
|
89
|
|
|
def check_species(self, column, item_set, country, create=False): |
|
90
|
|
|
"""Check if all species are defined in UID DictSpecies. Create |
|
91
|
|
|
dictionary term if create is True and species is not found""" |
|
92
|
|
|
|
|
93
|
|
|
check, not_found = self.check_items( |
|
94
|
|
|
item_set, DictSpecie, column) |
|
95
|
|
|
|
|
96
|
|
|
if check is False: |
|
97
|
|
|
# try to check in dictionary table |
|
98
|
|
|
logger.info("Searching for %s in dictionary tables" % (not_found)) |
|
99
|
|
|
|
|
100
|
|
|
# if this function return True, I found all synonyms |
|
101
|
|
|
if check_species_synonyms(not_found, country, create) is True: |
|
102
|
|
|
logger.info("Found %s in dictionary tables" % not_found) |
|
103
|
|
|
|
|
104
|
|
|
# return True and an empty list for check and not found items |
|
105
|
|
|
return True, [] |
|
106
|
|
|
|
|
107
|
|
|
else: |
|
108
|
|
|
# if I arrive here, there are species that I couldn't find |
|
109
|
|
|
logger.error( |
|
110
|
|
|
"Couldnt' find those species in dictionary tables:") |
|
111
|
|
|
logger.error(not_found) |
|
112
|
|
|
|
|
113
|
|
|
return check, not_found |
|
114
|
|
|
|
|
115
|
|
|
|
|
116
|
|
|
def get_or_create_obj(model, **kwargs): |
|
117
|
|
|
"""Generic method to create or getting a model object""" |
|
118
|
|
|
|
|
119
|
|
|
instance, created = model.objects.get_or_create(**kwargs) |
|
120
|
|
|
|
|
121
|
|
|
if created: |
|
122
|
|
|
logger.info("Created '%s'" % instance) |
|
123
|
|
|
|
|
124
|
|
|
else: |
|
125
|
|
|
logger.debug("Found '%s'" % instance) |
|
126
|
|
|
|
|
127
|
|
|
return instance |
|
128
|
|
|
|
|
129
|
|
|
|
|
130
|
|
|
def update_or_create_obj(model, **kwargs): |
|
131
|
|
|
"""Generic method to create or getting a model object""" |
|
132
|
|
|
|
|
133
|
|
|
if 'submission' in kwargs: |
|
134
|
|
|
# ok, try to remove submission from kwargs and test if this objects |
|
135
|
|
|
# is already in database |
|
136
|
|
|
new_kwargs = kwargs.copy() |
|
137
|
|
|
submission = new_kwargs.pop('submission') |
|
138
|
|
|
new_kwargs.pop('defaults') |
|
139
|
|
|
|
|
140
|
|
|
logger.debug("Test if %s is already in database" % (new_kwargs)) |
|
141
|
|
|
instance = model.objects.filter(**new_kwargs).first() |
|
142
|
|
|
|
|
143
|
|
|
if instance: |
|
144
|
|
|
logger.debug("Found %s in database" % (instance)) |
|
145
|
|
|
|
|
146
|
|
|
# test if instance is in a different submission |
|
147
|
|
|
if submission != instance.submission: |
|
148
|
|
|
message = ( |
|
149
|
|
|
"Ignoring: %s - Already in database with submission %s" |
|
150
|
|
|
% (kwargs, submission) |
|
151
|
|
|
) |
|
152
|
|
|
logger.warning(message) |
|
153
|
|
|
return instance |
|
154
|
|
|
|
|
155
|
|
|
# if I arrive here, or I don't have the submission key or |
|
156
|
|
|
# I see this object for the first time or I just see this |
|
157
|
|
|
# object in this submission |
|
158
|
|
|
instance, created = model.objects.update_or_create(**kwargs) |
|
159
|
|
|
|
|
160
|
|
|
if created: |
|
161
|
|
|
logger.debug("Created '%s'" % instance) |
|
162
|
|
|
|
|
163
|
|
|
else: |
|
164
|
|
|
logger.debug("Updating '%s'" % instance) |
|
165
|
|
|
|
|
166
|
|
|
return instance |
|
167
|
|
|
|
cnr-ibba /
IMAGE-InjectTool
