labimotion 0.3.1 → 0.3.2
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- checksums.yaml +4 -4
- data/lib/labimotion/{utils → collection}/export.rb +22 -11
- data/lib/labimotion/{utils → collection}/import.rb +53 -71
- data/lib/labimotion/entities/element_entity.rb +1 -0
- data/lib/labimotion/libs/converter.rb +36 -10
- data/lib/labimotion/libs/export_dataset.rb +8 -3
- data/lib/labimotion/libs/nmr_mapper.rb +35 -11
- data/lib/labimotion/models/concerns/attachment_converter.rb +16 -3
- data/lib/labimotion/models/element.rb +13 -6
- data/lib/labimotion/utils/import_utils.rb +116 -0
- data/lib/labimotion/version.rb +6 -2
- data/lib/labimotion.rb +5 -2
- metadata +7 -7
- data/lib/labimotion/api.rb +0 -19
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
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SHA256:
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: f27381a9c7cd989a1a7319548b244e69234aa77103569c9ed93d38364bed0703
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4
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+
data.tar.gz: 468793e841711b973122ef12abeb5767dad71a31e420c8a4d5b5e286a96da822
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 49d564f2cc9d32aa3f7ed3bb2dfda720f56a16fb111df201a3932d17c763ce91d3e261e809952e9f647348f02831fc5fa86ff94b163c5be23a7e76761db46625
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7
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+
data.tar.gz: 06c138de2c822f4be6ef8d4324bdcd439d845b247eff7e8e1e1eb0a7fc4d61742dedd9c196f047182e03955e3d573032c69a1525fed9f4bbea6c39851a18299e
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@@ -23,17 +23,20 @@ module Labimotion
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23
23
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end
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24
24
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25
25
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def self.fetch_elements(collection, segments, attachments, fetch_many, fetch_one, fetch_containers)
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26
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-
fetch_many.call(collection.elements, {
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27
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-
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28
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-
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29
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-
})
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30
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-
fetch_many.call(collection.collections_elements, {
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31
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-
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33
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-
})
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26
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+
# fetch_many.call(collection.elements, {
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27
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# 'element_klass_id' => 'Labimotion::ElementKlass',
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28
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+
# 'created_by' => 'User',
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29
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# })
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30
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+
# fetch_many.call(collection.collections_elements, {
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31
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+
# 'collection_id' => 'Collection',
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32
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+
# 'element_id' => 'Labimotion::Element',
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33
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+
# })
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34
34
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collection.elements.each do |element|
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35
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-
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36
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-
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35
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+
element, attachments = Labimotion::Export.fetch_properties(data, element, attachments, &fetch_one)
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36
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fetch_one.call(element, {
|
37
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+
'element_klass_id' => 'Labimotion::ElementKlass',
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38
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+
'created_by' => 'User',
|
39
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+
})
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37
40
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fetch_containers.call(element)
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38
41
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segment, @attachments = Labimotion::Export.fetch_segments(element, attachments, &fetch_one)
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39
42
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segments += segment if segment.present?
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@@ -91,6 +94,15 @@ module Labimotion
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|
91
94
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mol = Molecule.find(id) unless id.nil?
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92
95
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properties['layers'][key]['fields'][idx]['value']['el_id'] = fetch_one.call(mol) unless mol.nil?
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93
96
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end
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97
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+
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98
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+
field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
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99
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+
field_samples.each do |field|
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100
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+
# idx = properties['layers'][key]['fields'].index(field)
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+
# id = field["value"] && field["value"]["el_id"] unless idx.nil?
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102
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+
# ss = Sample.find(id) unless id.nil?
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103
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+
# properties['layers'][key]['fields'][idx]['value']['el_id'] = fetch_one.call(ss) unless ss.nil?
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104
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end
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105
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+
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94
106
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field_uploads = layer['fields'].select { |ss| ss['type'] == 'upload' }
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107
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field_uploads.each do |upload|
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idx = properties['layers'][key]['fields'].index(upload)
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@@ -123,7 +135,6 @@ module Labimotion
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123
135
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end
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136
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end
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end
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126
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-
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138
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end
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128
139
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instance.properties = properties
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[instance, attachments]
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@@ -1,5 +1,6 @@
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1
1
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# frozen_string_literal: true
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2
2
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3
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+
require 'labimotion/utils/import_utils'
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3
4
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module Labimotion
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4
5
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class Import
|
5
6
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@@ -50,7 +51,7 @@ module Labimotion
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50
51
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element_type = fields.fetch('element_type')
|
51
52
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element = instances.fetch(element_type).fetch(element_uuid)
|
52
53
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53
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-
dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id)
|
54
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+
dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id) if dk_id.present?
|
54
55
|
next if gt == true && dataset_klass.nil?
|
55
56
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56
57
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dkr = Labimotion::DatasetKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
|
@@ -88,33 +89,21 @@ module Labimotion
|
|
88
89
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ek_obj = data.fetch('Labimotion::ElementKlass').fetch(sk_obj["element_klass_id"])
|
89
90
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element_klass = Labimotion::ElementKlass.find_by(name: ek_obj['name']) if ek_obj.present?
|
90
91
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next if element_klass.nil? || ek_obj.nil? || ek_obj['is_generic'] == true
|
92
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+
|
91
93
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element_uuid = fields.fetch('element_id')
|
92
94
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element_type = fields.fetch('element_type')
|
93
95
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element = instances.fetch(element_type).fetch(element_uuid)
|
94
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-
segment_klass = Labimotion::SegmentKlass.find_by(identifier: sk_id)
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95
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
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-
# 'place',
|
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-
# 'properties_release',
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-
# 'uuid',
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-
# 'identifier',
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109
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-
# 'sync_time'
|
110
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-
# ).merge(
|
111
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-
# element_klass: element_klass,
|
112
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-
# created_by: current_user_id,
|
113
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-
# released_at: DateTime.now
|
114
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-
# )
|
115
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-
# ) if segment_klass.nil?
|
116
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-
|
117
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-
next if segment_klass.nil?
|
96
|
+
segment_klass = Labimotion::SegmentKlass.find_by(identifier: sk_id) if sk_id.present?
|
97
|
+
segment_klass = Labimotion::SegmentKlass.find_by(uuid: fields.fetch('klass_uuid')) if segment_klass.nil?
|
98
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+
|
99
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+
if segment_klass.nil?
|
100
|
+
skr = Labimotion::SegmentKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
|
101
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+
segment_klass = skr.segment_klass if segment_klass.nil? && skr.present?
|
102
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+
end
|
103
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+
|
104
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+
next if segment_klass.nil? || element.nil?
|
105
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+
|
106
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+
## segment_klass = Labimotion::ImportUtils.create_segment_klass(sk_obj, segment_klass, element_klass, current_user_id)
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118
107
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|
119
108
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segment = Labimotion::Segment.create!(
|
120
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fields.slice(
|
@@ -128,52 +117,7 @@ module Labimotion
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128
117
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)
|
129
118
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)
|
130
119
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|
131
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-
properties = segment.properties
|
132
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-
properties['layers'].keys.each do |key|
|
133
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-
layer = properties['layers'][key]
|
134
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-
field_molecules = layer['fields'].select { |ss| ss['type'] == 'drag_molecule' }
|
135
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-
field_molecules.each do |field|
|
136
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-
idx = properties['layers'][key]['fields'].index(field)
|
137
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-
id = field["value"] && field["value"]["el_id"] unless idx.nil?
|
138
|
-
mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
|
139
|
-
unless mol.nil?
|
140
|
-
properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
|
141
|
-
properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
|
142
|
-
properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
|
143
|
-
end
|
144
|
-
end
|
145
|
-
|
146
|
-
field_tables = layer['fields'].select { |ss| ss['type'] == 'table' }
|
147
|
-
field_tables&.each do |field|
|
148
|
-
tidx = layer['fields'].index(field)
|
149
|
-
next unless field['sub_values'].present? && field['sub_fields'].present?
|
150
|
-
|
151
|
-
field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
|
152
|
-
if field_table_molecules.present?
|
153
|
-
col_ids = field_table_molecules.map { |x| x.values[0] }
|
154
|
-
col_ids.each do |col_id|
|
155
|
-
field['sub_values'].each_with_index do |sub_value, vdx|
|
156
|
-
next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
|
157
|
-
|
158
|
-
svalue = sub_value[col_id]['value']
|
159
|
-
next unless svalue['el_id'].present? && svalue['el_inchikey'].present?
|
160
|
-
|
161
|
-
tmol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[svalue['el_id']]['molfile']) unless svalue['el_id'].nil?
|
162
|
-
unless tmol.nil?
|
163
|
-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_id'] = tmol.id
|
164
|
-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_tip'] = "#{tmol.inchikey}@@#{tmol.cano_smiles}"
|
165
|
-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_label'] = tmol.cano_smiles
|
166
|
-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_smiles'] = tmol.cano_smiles
|
167
|
-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_iupac'] = tmol.iupac_name
|
168
|
-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_inchikey'] = tmol.inchikey
|
169
|
-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_svg'] = File.join('/images', 'molecules', tmol.molecule_svg_file)
|
170
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-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_molecular_weight'] = tmol.molecular_weight
|
171
|
-
end
|
172
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-
end
|
173
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-
end
|
174
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-
end
|
175
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-
end
|
176
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-
end
|
120
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+
properties = Labimotion::ImportUtils.properties_handler(data, segment.properties)
|
177
121
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segment.update!(properties: properties)
|
178
122
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update_instances.call(uuid, segment)
|
179
123
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end
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@@ -182,5 +126,43 @@ module Labimotion
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182
126
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raise
|
183
127
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end
|
184
128
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end
|
129
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+
|
130
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+
def self.import_elements(data, instances, gt, current_user_id, fetch_many, &update_instances)
|
131
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+
data.fetch('Labimotion::Element', {}).each do |uuid, fields|
|
132
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+
klass_id = fields["element_klass_id"]
|
133
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+
ek_obj = data.fetch('Labimotion::ElementKlass', {})[klass_id]
|
134
|
+
ek_id = ek_obj["identifier"]
|
135
|
+
element_klass = Labimotion::ElementKlass.find_by(identifier: ek_id) if ek_id.present?
|
136
|
+
element_klass = Labimotion::ElementKlass.find_by(uuid: fields.fetch('klass_uuid')) if element_klass.nil?
|
137
|
+
|
138
|
+
if element_klass.nil?
|
139
|
+
ekr = Labimotion::ElementKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
|
140
|
+
element_klass = ekr.element_klass if element_klass.nil? && ekr.present?
|
141
|
+
end
|
142
|
+
next if element_klass.nil?
|
143
|
+
|
144
|
+
element = Labimotion::Element.create!(
|
145
|
+
fields.slice(
|
146
|
+
'name', 'properties', 'properties_release'
|
147
|
+
).merge(
|
148
|
+
created_by: current_user_id,
|
149
|
+
element_klass: element_klass,
|
150
|
+
collections: fetch_many.call(
|
151
|
+
'Collection', 'Labimotion::CollectionsElement', 'element_id', 'collection_id', uuid
|
152
|
+
),
|
153
|
+
uuid: SecureRandom.uuid,
|
154
|
+
klass_uuid: ekr&.uuid || element_klass.uuid
|
155
|
+
)
|
156
|
+
)
|
157
|
+
|
158
|
+
properties = Labimotion::ImportUtils.properties_handler(data, element.properties)
|
159
|
+
element.update!(properties: properties)
|
160
|
+
update_instances.call(uuid, element)
|
161
|
+
element.container = Container.create_root_container
|
162
|
+
end
|
163
|
+
rescue StandardError => e
|
164
|
+
Rails.logger.error(e.backtrace)
|
165
|
+
raise
|
166
|
+
end
|
185
167
|
end
|
186
168
|
end
|
@@ -14,11 +14,35 @@ require 'labimotion/utils/utils'
|
|
14
14
|
|
15
15
|
module Labimotion
|
16
16
|
class Converter
|
17
|
-
|
18
17
|
def self.logger
|
19
18
|
@@converter_logger ||= Logger.new(Rails.root.join('log/converter.log')) # rubocop:disable Style/ClassVars
|
20
19
|
end
|
21
20
|
|
21
|
+
def self.process_ds(id, current_user = {})
|
22
|
+
att = Attachment.find_by(attachable_id: id, con_state: Labimotion::ConState::CONVERTED)
|
23
|
+
return if att.nil?
|
24
|
+
|
25
|
+
dsr = []
|
26
|
+
ols = nil
|
27
|
+
|
28
|
+
Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
|
29
|
+
res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
|
30
|
+
ols = res[:o] unless res&.dig(:o).nil?
|
31
|
+
dsr.push(res[:d]) unless res&.dig(:d).nil?
|
32
|
+
end
|
33
|
+
dsr.flatten!
|
34
|
+
|
35
|
+
dataset = build_ds(id, ols)
|
36
|
+
update_ds(dataset, dsr, current_user) if dataset.present?
|
37
|
+
|
38
|
+
|
39
|
+
rescue StandardError => e
|
40
|
+
Labimotion::Converter.logger.error ["Att ID: #{att&.id}, OLS: #{ols}", "DSR: #{dsr}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
|
41
|
+
raise e
|
42
|
+
ensure
|
43
|
+
## tmp_file&.close
|
44
|
+
end
|
45
|
+
|
22
46
|
def self.uri(api_name)
|
23
47
|
url = Rails.configuration.converter.url
|
24
48
|
"#{url}#{api_name}"
|
@@ -126,15 +150,17 @@ module Labimotion
|
|
126
150
|
att.update!(storage: primary_store)
|
127
151
|
end
|
128
152
|
|
129
|
-
|
130
|
-
|
131
|
-
|
132
|
-
|
133
|
-
|
153
|
+
if Labimotion::IS_RAILS5 == true
|
154
|
+
Zip::File.open(tmp_file.path) do |zip_file|
|
155
|
+
res = Labimotion::Converter.collect_metadata(zip_file) if name.split('.')&.last == 'zip'
|
156
|
+
ols = res[:o] unless res&.dig(:o).nil?
|
157
|
+
dsr.push(res[:d]) unless res&.dig(:d).nil?
|
158
|
+
end
|
134
159
|
|
135
|
-
|
136
|
-
|
137
|
-
|
160
|
+
dsr.flatten!
|
161
|
+
if dsr.length.positive? && name.split('.')&.last == 'zip'
|
162
|
+
Labimotion::Converter.ts('write', att.attachable_id, ols: ols, info: dsr)
|
163
|
+
end
|
138
164
|
end
|
139
165
|
rescue StandardError => e
|
140
166
|
raise e
|
@@ -197,7 +223,7 @@ module Labimotion
|
|
197
223
|
begin
|
198
224
|
return unless dsr_info && dsr_info[:info]&.length.positive?
|
199
225
|
dataset = Labimotion::Converter.build_ds(att_id, dsr_info[:ols])
|
200
|
-
Labimotion::Converter.update_ds(dataset, dsr_info[:info], current_user)
|
226
|
+
Labimotion::Converter.update_ds(dataset, dsr_info[:info], current_user) if dataset.present?
|
201
227
|
rescue StandardError => e
|
202
228
|
Labimotion::Converter.logger.error ["Att ID: #{att_id}, OLS: #{dsr_info[:ols]}", "DSR: #{dsr_info[:info]}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
|
203
229
|
ensure
|
@@ -27,7 +27,7 @@ module Labimotion
|
|
27
27
|
name = ds.dataset_klass.label
|
28
28
|
|
29
29
|
match = name.match(/\((.*?)\)/)
|
30
|
-
name = match && match.length >
|
30
|
+
name = match && match.length > 1 ? match[1] : name
|
31
31
|
|
32
32
|
name = '1H NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000593'
|
33
33
|
name = '13C NMR' if ds.dataset_klass.ols_term_id == 'CHMO:0000595'
|
@@ -99,9 +99,14 @@ module Labimotion
|
|
99
99
|
wb = @xfile.workbook
|
100
100
|
gds = Labimotion::Dataset.find_by(element_id: id, element_type: 'Container')
|
101
101
|
cds = Container.find(id)
|
102
|
-
cds.attachments.where(aasm_state: 'csv')
|
102
|
+
cds_csv = cds.attachments.where(aasm_state: 'csv')
|
103
|
+
csv_length = cds_csv.length
|
104
|
+
return if csv_length.zero?
|
105
|
+
cds_csv.each_with_index do |att, idx|
|
103
106
|
name = File.basename(att.filename, '.csv')
|
104
|
-
|
107
|
+
name = name.slice(0, (25 - csv_length.to_s.length - 1))
|
108
|
+
sheet_name = "#{name}_#{idx}"
|
109
|
+
sheet = @xfile.workbook.add_worksheet(name: sheet_name)
|
105
110
|
|
106
111
|
if Labimotion::IS_RAILS5 == true
|
107
112
|
File.open(att.store.path) do |fi|
|
@@ -6,8 +6,22 @@ require 'labimotion/utils/utils'
|
|
6
6
|
module Labimotion
|
7
7
|
## NmrMapper
|
8
8
|
class NmrMapper
|
9
|
-
def self.
|
10
|
-
att = Attachment.
|
9
|
+
def self.process_ds(id, current_user = {})
|
10
|
+
att = Attachment.find_by(attachable_id: id, con_state: Labimotion::ConState::NMR)
|
11
|
+
return if att.nil?
|
12
|
+
|
13
|
+
content = is_brucker_binary(id, att)
|
14
|
+
if content.nil?
|
15
|
+
att.update_column(:con_state, Labimotion::ConState::NONE)
|
16
|
+
else
|
17
|
+
data = process(att, id, content)
|
18
|
+
generate_ds(id, data, current_user)
|
19
|
+
att.update_column(:con_state, Labimotion::ConState::PROCESSED)
|
20
|
+
end
|
21
|
+
end
|
22
|
+
|
23
|
+
def self.is_brucker_binary(id, att)
|
24
|
+
# att = Attachment.find(id)
|
11
25
|
if Labimotion::IS_RAILS5 == true
|
12
26
|
Zip::File.open(att.store.path) do |zip_file|
|
13
27
|
zip_file.each do |entry|
|
@@ -32,8 +46,9 @@ module Labimotion
|
|
32
46
|
nil
|
33
47
|
end
|
34
48
|
|
35
|
-
def self.process(id, content)
|
36
|
-
att
|
49
|
+
def self.process(att, id, content)
|
50
|
+
return if att.nil? || content.nil?
|
51
|
+
|
37
52
|
lines = content.split("\n").reject(&:empty?)
|
38
53
|
metadata = {}
|
39
54
|
lines.map do |ln|
|
@@ -42,18 +57,27 @@ module Labimotion
|
|
42
57
|
end
|
43
58
|
ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
|
44
59
|
ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
60
|
+
|
61
|
+
{ content: { metadata: metadata, ols: ols } }
|
62
|
+
# if content.present? && att.present?
|
63
|
+
# Labimotion::NmrMapper.ts('write', att.attachable_id,
|
64
|
+
# content: { metadata: metadata, ols: ols })
|
65
|
+
# end
|
49
66
|
end
|
50
67
|
|
51
68
|
def self.fetch_content(id)
|
52
|
-
|
69
|
+
atts = Attachment.where(attachable_id: id)
|
70
|
+
return if atts.nil?
|
71
|
+
|
72
|
+
atts.each do |att|
|
73
|
+
content = Labimotion::NmrMapper.ts('read', att.id)
|
74
|
+
return content if content.present?
|
75
|
+
end
|
53
76
|
end
|
54
77
|
|
55
|
-
|
56
|
-
|
78
|
+
|
79
|
+
def self.generate_ds(id, data, current_user = {})
|
80
|
+
# data = Labimotion::NmrMapper.fetch_content(id)
|
57
81
|
return if data.nil?
|
58
82
|
|
59
83
|
obj = Labimotion::NmrMapper.build_ds(id, data[:content])
|
@@ -22,15 +22,28 @@ module Labimotion
|
|
22
22
|
end
|
23
23
|
|
24
24
|
def exec_converter
|
25
|
+
return if self.has_attribute?(:con_state) == false || !con_state.present?
|
26
|
+
|
25
27
|
#return if attachable_id.nil?
|
26
|
-
return if
|
28
|
+
return if Labimotion::IS_RAILS5 == false && self.con_state != Labimotion::ConState::WAIT
|
29
|
+
|
30
|
+
return if self.has_attribute?(:con_state) == false || self.con_state.nil? || self.con_state == Labimotion::ConState::NONE
|
31
|
+
|
27
32
|
case con_state
|
28
33
|
when Labimotion::ConState::NMR
|
29
|
-
|
34
|
+
if Labimotion::IS_RAILS5 == true
|
35
|
+
content = Labimotion::NmrMapperRepo.is_brucker_binary(id)
|
36
|
+
else
|
37
|
+
content = Labimotion::NmrMapper.is_brucker_binary(id)
|
38
|
+
end
|
30
39
|
if content.nil?
|
31
40
|
self.con_state = Labimotion::ConState::NONE
|
32
41
|
else
|
33
|
-
Labimotion::
|
42
|
+
if Labimotion::IS_RAILS5 == true
|
43
|
+
Labimotion::NmrMapperRepo.process(id, content)
|
44
|
+
else
|
45
|
+
Labimotion::NmrMapper.process(id, content)
|
46
|
+
end
|
34
47
|
self.con_state = Labimotion::ConState::PROCESSED
|
35
48
|
end
|
36
49
|
when Labimotion::ConState::WAIT
|
@@ -101,13 +101,20 @@ module Labimotion
|
|
101
101
|
end
|
102
102
|
|
103
103
|
def thumb_svg
|
104
|
-
|
105
|
-
|
106
|
-
|
104
|
+
if Labimotion::IS_RAILS5 == true
|
105
|
+
image_atts = attachments.select do |a_img|
|
106
|
+
a_img&.content_type&.match(Regexp.union(%w[jpg jpeg png tiff tif]))
|
107
|
+
end
|
107
108
|
|
108
|
-
|
109
|
-
|
110
|
-
|
109
|
+
attachment = image_atts[0] || attachments[0]
|
110
|
+
preview = attachment.read_thumbnail if attachment
|
111
|
+
preview && Base64.encode64(preview) || 'not available'
|
112
|
+
else
|
113
|
+
image_atts = attachments.select(&:type_image?)
|
114
|
+
attachment = image_atts[0] || attachments[0]
|
115
|
+
preview = attachment&.read_thumbnail
|
116
|
+
(preview && Base64.encode64(preview)) || 'not available'
|
117
|
+
end
|
111
118
|
end
|
112
119
|
|
113
120
|
|
@@ -0,0 +1,116 @@
|
|
1
|
+
# frozen_string_literal: true
|
2
|
+
|
3
|
+
module Labimotion
|
4
|
+
## Import Utils
|
5
|
+
class ImportUtils
|
6
|
+
def self.proc_sample(layer, key, data, properties)
|
7
|
+
field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
|
8
|
+
field_samples.each do |field|
|
9
|
+
idx = properties['layers'][key]['fields'].index(field)
|
10
|
+
id = field["value"] && field["value"]["el_id"] unless idx.nil?
|
11
|
+
|
12
|
+
# mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
|
13
|
+
# unless mol.nil?
|
14
|
+
# properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
|
15
|
+
# properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
|
16
|
+
# properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
|
17
|
+
# end
|
18
|
+
end
|
19
|
+
properties
|
20
|
+
rescue StandardError => e
|
21
|
+
Rails.logger.error(e.backtrace)
|
22
|
+
raise
|
23
|
+
end
|
24
|
+
|
25
|
+
def self.proc_molecule(layer, key, data, properties)
|
26
|
+
field_molecules = layer['fields'].select { |ss| ss['type'] == 'drag_molecule' }
|
27
|
+
field_molecules.each do |field|
|
28
|
+
idx = properties['layers'][key]['fields'].index(field)
|
29
|
+
id = field["value"] && field["value"]["el_id"] unless idx.nil?
|
30
|
+
mol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[id]['molfile']) unless id.nil?
|
31
|
+
unless mol.nil?
|
32
|
+
properties['layers'][key]['fields'][idx]['value']['el_id'] = mol.id
|
33
|
+
properties['layers'][key]['fields'][idx]['value']['el_tip'] = "#{mol.inchikey}@@#{mol.cano_smiles}"
|
34
|
+
properties['layers'][key]['fields'][idx]['value']['el_label'] = mol.iupac_name
|
35
|
+
end
|
36
|
+
end
|
37
|
+
properties
|
38
|
+
rescue StandardError => e
|
39
|
+
Rails.logger.error(e.backtrace)
|
40
|
+
raise
|
41
|
+
end
|
42
|
+
|
43
|
+
def self.proc_table(layer, key, data, properties)
|
44
|
+
field_tables = layer['fields'].select { |ss| ss['type'] == 'table' }
|
45
|
+
field_tables&.each do |field|
|
46
|
+
tidx = layer['fields'].index(field)
|
47
|
+
next unless field['sub_values'].present? && field['sub_fields'].present?
|
48
|
+
|
49
|
+
field_table_molecules = field['sub_fields'].select { |ss| ss['type'] == 'drag_molecule' }
|
50
|
+
if field_table_molecules.present?
|
51
|
+
col_ids = field_table_molecules.map { |x| x.values[0] }
|
52
|
+
col_ids.each do |col_id|
|
53
|
+
field['sub_values'].each_with_index do |sub_value, vdx|
|
54
|
+
next unless sub_value[col_id].present? && sub_value[col_id]['value'].present? && sub_value[col_id]['value']['el_id'].present?
|
55
|
+
|
56
|
+
svalue = sub_value[col_id]['value']
|
57
|
+
next unless svalue['el_id'].present? && svalue['el_inchikey'].present?
|
58
|
+
|
59
|
+
tmol = Molecule.find_or_create_by_molfile(data.fetch('Molecule')[svalue['el_id']]['molfile']) unless svalue['el_id'].nil?
|
60
|
+
unless tmol.nil?
|
61
|
+
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_id'] = tmol.id
|
62
|
+
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_tip'] = "#{tmol.inchikey}@@#{tmol.cano_smiles}"
|
63
|
+
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_label'] = tmol.cano_smiles
|
64
|
+
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_smiles'] = tmol.cano_smiles
|
65
|
+
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_iupac'] = tmol.iupac_name
|
66
|
+
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_inchikey'] = tmol.inchikey
|
67
|
+
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_svg'] = File.join('/images', 'molecules', tmol.molecule_svg_file)
|
68
|
+
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_molecular_weight'] = tmol.molecular_weight
|
69
|
+
end
|
70
|
+
end
|
71
|
+
end
|
72
|
+
end
|
73
|
+
end
|
74
|
+
properties
|
75
|
+
rescue StandardError => e
|
76
|
+
Rails.logger.error(e.backtrace)
|
77
|
+
raise
|
78
|
+
end
|
79
|
+
|
80
|
+
def self.properties_handler(data, properties)
|
81
|
+
properties && properties['layers'] && properties['layers'].keys&.each do |key|
|
82
|
+
layer = properties['layers'][key]
|
83
|
+
properties = proc_molecule(layer, key, data, properties)
|
84
|
+
properties = proc_table(layer, key, data, properties)
|
85
|
+
# properties = proc_sample(layer, key, data, properties)
|
86
|
+
end
|
87
|
+
properties
|
88
|
+
rescue StandardError => e
|
89
|
+
Rails.logger.error(e.backtrace)
|
90
|
+
raise
|
91
|
+
end
|
92
|
+
|
93
|
+
def self.create_segment_klass(sk_obj, segment_klass, element_klass, current_user_id)
|
94
|
+
return if segment_klass.present? || element_klass.nil? || sk_obj.nil?
|
95
|
+
|
96
|
+
segment_klass = Labimotion::SegmentKlass.create!(sk_obj.slice(
|
97
|
+
'label',
|
98
|
+
'desc',
|
99
|
+
'properties_template',
|
100
|
+
'is_active',
|
101
|
+
'place',
|
102
|
+
'properties_release',
|
103
|
+
'uuid',
|
104
|
+
'identifier',
|
105
|
+
'sync_time'
|
106
|
+
).merge(
|
107
|
+
element_klass: element_klass,
|
108
|
+
created_by: current_user_id,
|
109
|
+
released_at: DateTime.now
|
110
|
+
)
|
111
|
+
)
|
112
|
+
|
113
|
+
segment_klass
|
114
|
+
end
|
115
|
+
end
|
116
|
+
end
|
data/lib/labimotion/version.rb
CHANGED
@@ -1,7 +1,11 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
|
+
## Labimotion Version
|
3
4
|
module Labimotion
|
4
5
|
IS_RAILS5 = true
|
5
|
-
|
6
|
-
|
6
|
+
VERSION_ELN = '1.0.13'
|
7
|
+
VERSION_REPO = '0.3.2'
|
8
|
+
|
9
|
+
VERSION = Labimotion::VERSION_REPO if Labimotion::IS_RAILS5 == true
|
10
|
+
VERSION = Labimotion::VERSION_ELN if Labimotion::IS_RAILS5 == false
|
7
11
|
end
|
data/lib/labimotion.rb
CHANGED
@@ -61,8 +61,11 @@ module Labimotion
|
|
61
61
|
autoload :ConState, 'labimotion/utils/con_state'
|
62
62
|
autoload :Serializer, 'labimotion/utils/serializer'
|
63
63
|
autoload :Search, 'labimotion/utils/search'
|
64
|
-
|
65
|
-
|
64
|
+
|
65
|
+
|
66
|
+
######## Collection
|
67
|
+
autoload :Export, 'labimotion/collection/export'
|
68
|
+
autoload :Import, 'labimotion/collection/import'
|
66
69
|
|
67
70
|
######## Models
|
68
71
|
autoload :Element, 'labimotion/models/element'
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: labimotion
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.3.
|
4
|
+
version: 0.3.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Chia-Lin Lin
|
@@ -9,7 +9,7 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2023-
|
12
|
+
date: 2023-10-16 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: rails
|
@@ -34,12 +34,13 @@ extensions: []
|
|
34
34
|
extra_rdoc_files: []
|
35
35
|
files:
|
36
36
|
- lib/labimotion.rb
|
37
|
-
- lib/labimotion/api.rb
|
38
37
|
- lib/labimotion/apis/converter_api.rb
|
39
38
|
- lib/labimotion/apis/generic_dataset_api.rb
|
40
39
|
- lib/labimotion/apis/generic_element_api.rb
|
41
40
|
- lib/labimotion/apis/labimotion_hub_api.rb
|
42
41
|
- lib/labimotion/apis/segment_api.rb
|
42
|
+
- lib/labimotion/collection/export.rb
|
43
|
+
- lib/labimotion/collection/import.rb
|
43
44
|
- lib/labimotion/entities/application_entity.rb
|
44
45
|
- lib/labimotion/entities/dataset_entity.rb
|
45
46
|
- lib/labimotion/entities/dataset_klass_entity.rb
|
@@ -90,15 +91,14 @@ files:
|
|
90
91
|
- lib/labimotion/models/segment_klasses_revision.rb
|
91
92
|
- lib/labimotion/models/segments_revision.rb
|
92
93
|
- lib/labimotion/utils/con_state.rb
|
93
|
-
- lib/labimotion/utils/
|
94
|
-
- lib/labimotion/utils/import.rb
|
94
|
+
- lib/labimotion/utils/import_utils.rb
|
95
95
|
- lib/labimotion/utils/search.rb
|
96
96
|
- lib/labimotion/utils/serializer.rb
|
97
97
|
- lib/labimotion/utils/utils.rb
|
98
98
|
- lib/labimotion/version.rb
|
99
|
-
homepage: https://
|
99
|
+
homepage: https://gitlab.kit.edu/kit/labimotion/labimotion
|
100
100
|
licenses:
|
101
|
-
-
|
101
|
+
- GPL-3.0
|
102
102
|
metadata: {}
|
103
103
|
post_install_message:
|
104
104
|
rdoc_options: []
|
data/lib/labimotion/api.rb
DELETED
@@ -1,19 +0,0 @@
|
|
1
|
-
# frozen_string_literal: true
|
2
|
-
|
3
|
-
## This is the first version of the dataset class
|
4
|
-
module Labimotion
|
5
|
-
## This is the first version of the dataset class
|
6
|
-
class Api
|
7
|
-
def initialize
|
8
|
-
# Initialization code
|
9
|
-
end
|
10
|
-
|
11
|
-
def gget_data
|
12
|
-
'Hello, worlddddddddddddddddddddd!'
|
13
|
-
end
|
14
|
-
|
15
|
-
def self.hello
|
16
|
-
'Hellooooooooooooooooooooo!'
|
17
|
-
end
|
18
|
-
end
|
19
|
-
end
|