|
1
|
|
|
#!/usr/bin/env python3 |
|
2
|
|
|
# -*- coding: utf-8 -*- |
|
3
|
|
|
""" |
|
4
|
|
|
Created on Mon May 7 15:49:04 2018 |
|
5
|
|
|
|
|
6
|
|
|
@author: Paolo Cozzi <[email protected]> |
|
7
|
|
|
|
|
8
|
|
|
Functions adapted from Jun Fan misc.py and use_zooma.py python scripts |
|
9
|
|
|
""" |
|
10
|
|
|
|
|
11
|
|
|
import logging |
|
12
|
|
|
|
|
13
|
|
|
from image_validation.use_ontology import use_zooma |
|
14
|
|
|
|
|
15
|
|
|
from common.constants import CONFIDENCES |
|
16
|
|
|
|
|
17
|
|
|
|
|
18
|
|
|
# Get an instance of a logger |
|
19
|
|
|
logger = logging.getLogger(__name__) |
|
20
|
|
|
|
|
21
|
|
|
|
|
22
|
|
|
def annotate_generic(model, zooma_type): |
|
23
|
|
|
"""Annotate a generic DictTable |
|
24
|
|
|
|
|
25
|
|
|
Args: |
|
26
|
|
|
model (:py:class:`image_app.models.DictBase`): A DictBase istance |
|
27
|
|
|
zooma_type (str): the type of zooma annotation (country, species, ...) |
|
28
|
|
|
""" |
|
29
|
|
|
|
|
30
|
|
|
logger.debug("Processing %s" % (model)) |
|
31
|
|
|
|
|
32
|
|
|
result = use_zooma(model.label, zooma_type) |
|
33
|
|
|
|
|
34
|
|
|
# update object (if possible) |
|
35
|
|
|
if result: |
|
36
|
|
|
url = result['ontologyTerms'] |
|
37
|
|
|
# https://stackoverflow.com/a/7253830 |
|
38
|
|
|
term = url.rsplit('/', 1)[-1] |
|
39
|
|
|
|
|
40
|
|
|
# The ontology seems correct. Annotate! |
|
41
|
|
|
logger.info("Updating %s with %s" % (model, result)) |
|
42
|
|
|
url = result['ontologyTerms'] |
|
43
|
|
|
|
|
44
|
|
|
model.term = term |
|
45
|
|
|
|
|
46
|
|
|
# get an int object for such confidence |
|
47
|
|
|
confidence = CONFIDENCES.get_value( |
|
48
|
|
|
result["confidence"].lower()) |
|
49
|
|
|
|
|
50
|
|
|
model.confidence = confidence |
|
51
|
|
|
model.save() |
|
52
|
|
|
|
|
53
|
|
|
|
|
54
|
|
|
def annotate_country(country_obj): |
|
55
|
|
|
"""Annotate a country object using Zooma""" |
|
56
|
|
|
|
|
57
|
|
|
annotate_generic(country_obj, "country") |
|
58
|
|
|
|
|
59
|
|
|
|
|
60
|
|
|
def annotate_breed(breed_obj): |
|
61
|
|
|
"""Annotate a breed object using Zooma""" |
|
62
|
|
|
|
|
63
|
|
|
logger.debug("Processing %s" % (breed_obj)) |
|
64
|
|
|
|
|
65
|
|
|
result = use_zooma( |
|
66
|
|
|
breed_obj.supplied_breed, "breed") |
|
67
|
|
|
|
|
68
|
|
|
# update object (if possible) |
|
69
|
|
|
if result: |
|
70
|
|
|
url = result['ontologyTerms'] |
|
71
|
|
|
# https://stackoverflow.com/a/7253830 |
|
72
|
|
|
term = url.rsplit('/', 1)[-1] |
|
73
|
|
|
|
|
74
|
|
|
# The ontology seems correct. Annotate! |
|
75
|
|
|
logger.info("Updating %s with %s" % (breed_obj, result)) |
|
76
|
|
|
url = result['ontologyTerms'] |
|
77
|
|
|
|
|
78
|
|
|
# this is slight different from annotate_generic |
|
79
|
|
|
breed_obj.mapped_breed_term = term |
|
80
|
|
|
breed_obj.mapped_breed = result['text'] |
|
81
|
|
|
|
|
82
|
|
|
# get an int object for such confidence |
|
83
|
|
|
confidence = CONFIDENCES.get_value( |
|
84
|
|
|
result["confidence"].lower()) |
|
85
|
|
|
|
|
86
|
|
|
breed_obj.confidence = confidence |
|
87
|
|
|
breed_obj.save() |
|
88
|
|
|
|
|
89
|
|
|
|
|
90
|
|
|
def annotate_specie(specie_obj): |
|
91
|
|
|
"""Annotate a specie object using Zooma""" |
|
92
|
|
|
|
|
93
|
|
|
annotate_generic(specie_obj, "species") |
|
94
|
|
|
|
|
95
|
|
|
|
|
96
|
|
|
def annotate_uberon(uberon_obj): |
|
97
|
|
|
"""Annotate an organism part object using Zooma""" |
|
98
|
|
|
|
|
99
|
|
|
annotate_generic(uberon_obj, "organism part") |
|
100
|
|
|
|
cnr-ibba /
IMAGE-InjectTool
