labimotion 0.3.1 → 0.3.3
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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 +46 -23
- data/lib/labimotion/libs/export_dataset.rb +8 -3
- data/lib/labimotion/libs/nmr_mapper.rb +39 -15
- data/lib/labimotion/models/concerns/attachment_converter.rb +10 -10
- 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 -8
- data/lib/labimotion/api.rb +0 -19
- data/lib/labimotion/libs/nmr_mapper_repo.rb +0 -278
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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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: 1e2976eacd1dbe12aa1caefd59638628b544d64ebd2757b677bc527e18230c1c
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4
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+
data.tar.gz: f1ee1381e67ab62bd66b4178f25346988c471b34c1da917e010e7753a83279ca
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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: e8d3ca3477cfecd469e1d5e1a41be249a5b69da8647478ebd24a6144498dc5a110a4976f6cec56f10bc6fca013872dba164aa47be7402d511219a50d78ce8309
|
7
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+
data.tar.gz: c6098201eb9ef587b0201e35c56b1146697e19dfead041aad7fb2b515ed4e38db2c00051508b0d631faeb979fc62edb287add0ad9be76c243da30d69d8230949
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@@ -23,17 +23,20 @@ module Labimotion
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|
23
23
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end
|
24
24
|
|
25
25
|
def self.fetch_elements(collection, segments, attachments, fetch_many, fetch_one, fetch_containers)
|
26
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-
fetch_many.call(collection.elements, {
|
27
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-
|
28
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-
|
29
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-
})
|
30
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-
fetch_many.call(collection.collections_elements, {
|
31
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-
|
32
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-
|
33
|
-
})
|
26
|
+
# fetch_many.call(collection.elements, {
|
27
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+
# 'element_klass_id' => 'Labimotion::ElementKlass',
|
28
|
+
# 'created_by' => 'User',
|
29
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+
# })
|
30
|
+
# fetch_many.call(collection.collections_elements, {
|
31
|
+
# 'collection_id' => 'Collection',
|
32
|
+
# 'element_id' => 'Labimotion::Element',
|
33
|
+
# })
|
34
34
|
collection.elements.each do |element|
|
35
|
-
|
36
|
-
|
35
|
+
element, attachments = Labimotion::Export.fetch_properties(data, element, attachments, &fetch_one)
|
36
|
+
fetch_one.call(element, {
|
37
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+
'element_klass_id' => 'Labimotion::ElementKlass',
|
38
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+
'created_by' => 'User',
|
39
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+
})
|
37
40
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fetch_containers.call(element)
|
38
41
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segment, @attachments = Labimotion::Export.fetch_segments(element, attachments, &fetch_one)
|
39
42
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segments += segment if segment.present?
|
@@ -91,6 +94,15 @@ module Labimotion
|
|
91
94
|
mol = Molecule.find(id) unless id.nil?
|
92
95
|
properties['layers'][key]['fields'][idx]['value']['el_id'] = fetch_one.call(mol) unless mol.nil?
|
93
96
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end
|
97
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+
|
98
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+
field_samples = layer['fields'].select { |ss| ss['type'] == 'drag_sample' }
|
99
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+
field_samples.each do |field|
|
100
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+
# idx = properties['layers'][key]['fields'].index(field)
|
101
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+
# id = field["value"] && field["value"]["el_id"] unless idx.nil?
|
102
|
+
# ss = Sample.find(id) unless id.nil?
|
103
|
+
# properties['layers'][key]['fields'][idx]['value']['el_id'] = fetch_one.call(ss) unless ss.nil?
|
104
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+
end
|
105
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+
|
94
106
|
field_uploads = layer['fields'].select { |ss| ss['type'] == 'upload' }
|
95
107
|
field_uploads.each do |upload|
|
96
108
|
idx = properties['layers'][key]['fields'].index(upload)
|
@@ -123,7 +135,6 @@ module Labimotion
|
|
123
135
|
end
|
124
136
|
end
|
125
137
|
end
|
126
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-
|
127
138
|
end
|
128
139
|
instance.properties = properties
|
129
140
|
[instance, attachments]
|
@@ -1,5 +1,6 @@
|
|
1
1
|
# frozen_string_literal: true
|
2
2
|
|
3
|
+
require 'labimotion/utils/import_utils'
|
3
4
|
module Labimotion
|
4
5
|
class Import
|
5
6
|
|
@@ -50,7 +51,7 @@ module Labimotion
|
|
50
51
|
element_type = fields.fetch('element_type')
|
51
52
|
element = instances.fetch(element_type).fetch(element_uuid)
|
52
53
|
|
53
|
-
dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id)
|
54
|
+
dataset_klass = Labimotion::DatasetKlass.find_by(identifier: dk_id) if dk_id.present?
|
54
55
|
next if gt == true && dataset_klass.nil?
|
55
56
|
|
56
57
|
dkr = Labimotion::DatasetKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
|
@@ -88,33 +89,21 @@ module Labimotion
|
|
88
89
|
ek_obj = data.fetch('Labimotion::ElementKlass').fetch(sk_obj["element_klass_id"])
|
89
90
|
element_klass = Labimotion::ElementKlass.find_by(name: ek_obj['name']) if ek_obj.present?
|
90
91
|
next if element_klass.nil? || ek_obj.nil? || ek_obj['is_generic'] == true
|
92
|
+
|
91
93
|
element_uuid = fields.fetch('element_id')
|
92
94
|
element_type = fields.fetch('element_type')
|
93
95
|
element = instances.fetch(element_type).fetch(element_uuid)
|
94
|
-
segment_klass = Labimotion::SegmentKlass.find_by(identifier: sk_id)
|
95
|
-
|
96
|
-
|
97
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-
|
98
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-
|
99
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-
|
100
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-
|
101
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-
|
102
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-
|
103
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-
|
104
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-
|
105
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-
# 'place',
|
106
|
-
# 'properties_release',
|
107
|
-
# 'uuid',
|
108
|
-
# 'identifier',
|
109
|
-
# 'sync_time'
|
110
|
-
# ).merge(
|
111
|
-
# element_klass: element_klass,
|
112
|
-
# created_by: current_user_id,
|
113
|
-
# released_at: DateTime.now
|
114
|
-
# )
|
115
|
-
# ) if segment_klass.nil?
|
116
|
-
|
117
|
-
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
|
+
|
99
|
+
if segment_klass.nil?
|
100
|
+
skr = Labimotion::SegmentKlassesRevision.find_by(uuid: fields.fetch('klass_uuid'))
|
101
|
+
segment_klass = skr.segment_klass if segment_klass.nil? && skr.present?
|
102
|
+
end
|
103
|
+
|
104
|
+
next if segment_klass.nil? || element.nil?
|
105
|
+
|
106
|
+
## segment_klass = Labimotion::ImportUtils.create_segment_klass(sk_obj, segment_klass, element_klass, current_user_id)
|
118
107
|
|
119
108
|
segment = Labimotion::Segment.create!(
|
120
109
|
fields.slice(
|
@@ -128,52 +117,7 @@ module Labimotion
|
|
128
117
|
)
|
129
118
|
)
|
130
119
|
|
131
|
-
properties = segment.properties
|
132
|
-
properties['layers'].keys.each do |key|
|
133
|
-
layer = properties['layers'][key]
|
134
|
-
field_molecules = layer['fields'].select { |ss| ss['type'] == 'drag_molecule' }
|
135
|
-
field_molecules.each do |field|
|
136
|
-
idx = properties['layers'][key]['fields'].index(field)
|
137
|
-
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
|
-
properties['layers'][key]['fields'][tidx]['sub_values'][vdx][col_id]['value']['el_molecular_weight'] = tmol.molecular_weight
|
171
|
-
end
|
172
|
-
end
|
173
|
-
end
|
174
|
-
end
|
175
|
-
end
|
176
|
-
end
|
120
|
+
properties = Labimotion::ImportUtils.properties_handler(data, segment.properties)
|
177
121
|
segment.update!(properties: properties)
|
178
122
|
update_instances.call(uuid, segment)
|
179
123
|
end
|
@@ -182,5 +126,43 @@ module Labimotion
|
|
182
126
|
raise
|
183
127
|
end
|
184
128
|
end
|
129
|
+
|
130
|
+
def self.import_elements(data, instances, gt, current_user_id, fetch_many, &update_instances)
|
131
|
+
data.fetch('Labimotion::Element', {}).each do |uuid, fields|
|
132
|
+
klass_id = fields["element_klass_id"]
|
133
|
+
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 +14,38 @@ 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(id: id, con_state: Labimotion::ConState::CONVERTED)
|
23
|
+
return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
|
24
|
+
|
25
|
+
dsr = []
|
26
|
+
ols = nil
|
27
|
+
if Labimotion::IS_RAILS5 == true
|
28
|
+
Zip::File.open(att.store.path) 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
|
+
else
|
34
|
+
Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
|
35
|
+
res = Labimotion::Converter.collect_metadata(zip_file) if att.filename.split('.')&.last == 'zip'
|
36
|
+
ols = res[:o] unless res&.dig(:o).nil?
|
37
|
+
dsr.push(res[:d]) unless res&.dig(:d).nil?
|
38
|
+
end
|
39
|
+
end
|
40
|
+
dsr.flatten!
|
41
|
+
dataset = build_ds(att.attachable_id, ols)
|
42
|
+
update_ds(dataset, dsr, current_user) if dataset.present?
|
43
|
+
att.update_column(:con_state, Labimotion::ConState::COMPLETED)
|
44
|
+
rescue StandardError => e
|
45
|
+
Labimotion::Converter.logger.error ["Att ID: #{att&.id}, OLS: #{ols}", "DSR: #{dsr}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
|
46
|
+
raise e
|
47
|
+
end
|
48
|
+
|
22
49
|
def self.uri(api_name)
|
23
50
|
url = Rails.configuration.converter.url
|
24
51
|
"#{url}#{api_name}"
|
@@ -125,17 +152,7 @@ module Labimotion
|
|
125
152
|
primary_store = Rails.configuration.storage.primary_store
|
126
153
|
att.update!(storage: primary_store)
|
127
154
|
end
|
128
|
-
|
129
|
-
Zip::File.open(tmp_file.path) do |zip_file|
|
130
|
-
res = Labimotion::Converter.collect_metadata(zip_file) if name.split('.')&.last == 'zip'
|
131
|
-
ols = res[:o] unless res&.dig(:o).nil?
|
132
|
-
dsr.push(res[:d]) unless res&.dig(:d).nil?
|
133
|
-
end
|
134
|
-
|
135
|
-
dsr.flatten!
|
136
|
-
if dsr.length.positive? && name.split('.')&.last == 'zip'
|
137
|
-
Labimotion::Converter.ts('write', att.attachable_id, ols: ols, info: dsr)
|
138
|
-
end
|
155
|
+
process_ds(att.id)
|
139
156
|
rescue StandardError => e
|
140
157
|
raise e
|
141
158
|
ensure
|
@@ -179,25 +196,22 @@ module Labimotion
|
|
179
196
|
end
|
180
197
|
|
181
198
|
def self.jcamp_converter(id)
|
182
|
-
|
183
|
-
|
184
|
-
|
185
|
-
data = Labimotion::Converter.vor_conv(id)
|
186
|
-
return if data.nil?
|
199
|
+
data = Labimotion::Converter.vor_conv(id)
|
200
|
+
return if data.nil?
|
187
201
|
|
188
|
-
|
189
|
-
|
190
|
-
|
191
|
-
|
192
|
-
end
|
202
|
+
Labimotion::Converter.process(data)
|
203
|
+
rescue StandardError => e
|
204
|
+
Labimotion::Converter.logger.error ["jcamp_converter fail: #{id}", e.message, *e.backtrace].join($INPUT_RECORD_SEPARATOR)
|
205
|
+
Labimotion::ConState::ERROR
|
193
206
|
end
|
194
207
|
|
195
208
|
def self.generate_ds(att_id, current_user = {})
|
196
209
|
dsr_info = Labimotion::Converter.fetch_dsr(att_id)
|
197
210
|
begin
|
198
211
|
return unless dsr_info && dsr_info[:info]&.length.positive?
|
212
|
+
|
199
213
|
dataset = Labimotion::Converter.build_ds(att_id, dsr_info[:ols])
|
200
|
-
Labimotion::Converter.update_ds(dataset, dsr_info[:info], current_user)
|
214
|
+
Labimotion::Converter.update_ds(dataset, dsr_info[:info], current_user) if dataset.present?
|
201
215
|
rescue StandardError => e
|
202
216
|
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
217
|
ensure
|
@@ -325,6 +339,15 @@ module Labimotion
|
|
325
339
|
end
|
326
340
|
res
|
327
341
|
end
|
342
|
+
|
343
|
+
def self.metadata(id)
|
344
|
+
att = Attachment.find(id)
|
345
|
+
return if att.nil? || att.attachable_id.nil? || att.attachable_type != 'Container'
|
346
|
+
|
347
|
+
ds = Labimotion::Dataset.find_by(element_type: 'Container', element_id: att.attachable_id)
|
348
|
+
att.update_column(:con_state, Labimotion::ConState::COMPLETED) if ds.present?
|
349
|
+
process_ds(att.id) if ds.nil?
|
350
|
+
end
|
328
351
|
end
|
329
352
|
end
|
330
353
|
|
@@ -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 +6,24 @@ require 'labimotion/utils/utils'
|
|
6
6
|
module Labimotion
|
7
7
|
## NmrMapper
|
8
8
|
class NmrMapper
|
9
|
+
def self.process_ds(id, current_user = {})
|
10
|
+
att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
|
11
|
+
return if att.nil?
|
12
|
+
|
13
|
+
content = is_brucker_binary(id)
|
14
|
+
if content.nil?
|
15
|
+
Labimotion::ConState::NONE
|
16
|
+
else
|
17
|
+
data = process(att, id, content)
|
18
|
+
generate_ds(id, att.attachable_id, data, current_user)
|
19
|
+
Labimotion::ConState::COMPLETED
|
20
|
+
end
|
21
|
+
end
|
22
|
+
|
9
23
|
def self.is_brucker_binary(id)
|
10
|
-
att = Attachment.
|
24
|
+
att = Attachment.find_by(id: id, con_state: Labimotion::ConState::NMR)
|
25
|
+
return if att.nil?
|
26
|
+
|
11
27
|
if Labimotion::IS_RAILS5 == true
|
12
28
|
Zip::File.open(att.store.path) do |zip_file|
|
13
29
|
zip_file.each do |entry|
|
@@ -32,8 +48,9 @@ module Labimotion
|
|
32
48
|
nil
|
33
49
|
end
|
34
50
|
|
35
|
-
def self.process(id, content)
|
36
|
-
att
|
51
|
+
def self.process(att, id, content)
|
52
|
+
return if att.nil? || content.nil?
|
53
|
+
|
37
54
|
lines = content.split("\n").reject(&:empty?)
|
38
55
|
metadata = {}
|
39
56
|
lines.map do |ln|
|
@@ -42,26 +59,33 @@ module Labimotion
|
|
42
59
|
end
|
43
60
|
ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
|
44
61
|
ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
62
|
+
|
63
|
+
{ content: { metadata: metadata, ols: ols } }
|
64
|
+
# if content.present? && att.present?
|
65
|
+
# Labimotion::NmrMapper.ts('write', att.attachable_id,
|
66
|
+
# content: { metadata: metadata, ols: ols })
|
67
|
+
# end
|
49
68
|
end
|
50
69
|
|
51
70
|
def self.fetch_content(id)
|
52
|
-
|
71
|
+
atts = Attachment.where(attachable_id: id)
|
72
|
+
return if atts.nil?
|
73
|
+
|
74
|
+
atts.each do |att|
|
75
|
+
content = Labimotion::NmrMapper.ts('read', att.id)
|
76
|
+
return content if content.present?
|
77
|
+
end
|
53
78
|
end
|
54
79
|
|
55
|
-
def self.generate_ds(id, current_user = {})
|
56
|
-
data = Labimotion::NmrMapper.fetch_content(id)
|
57
|
-
return if data.nil?
|
58
80
|
|
59
|
-
|
81
|
+
def self.generate_ds(id, cid, data, current_user = {})
|
82
|
+
return if data.nil? || cid.nil?
|
83
|
+
|
84
|
+
obj = Labimotion::NmrMapper.build_ds(cid, data[:content])
|
60
85
|
return if obj.nil? || obj[:ols].nil?
|
61
86
|
|
62
|
-
Labimotion::NmrMapper.update_ds_1h(
|
63
|
-
Labimotion::NmrMapper.update_ds_1h(
|
64
|
-
Labimotion::NmrMapper.clean(id)
|
87
|
+
Labimotion::NmrMapper.update_ds_1h(cid, obj, current_user) if obj[:ols] == 'CHMO:0000593'
|
88
|
+
Labimotion::NmrMapper.update_ds_1h(cid, obj, current_user) if obj[:ols] == 'CHMO:0000595'
|
65
89
|
end
|
66
90
|
|
67
91
|
def self.update_ds_13c(id, obj)
|
@@ -10,6 +10,7 @@ module Labimotion
|
|
10
10
|
after_update :exec_converter
|
11
11
|
def init_converter
|
12
12
|
return if self.has_attribute?(:con_state) == false || con_state.present?
|
13
|
+
|
13
14
|
if Rails.configuration.try(:converter).try(:url) && ACCEPTED_FORMATS.include?(File.extname(filename&.downcase))
|
14
15
|
self.con_state = Labimotion::ConState::WAIT
|
15
16
|
end
|
@@ -22,21 +23,20 @@ module Labimotion
|
|
22
23
|
end
|
23
24
|
|
24
25
|
def exec_converter
|
25
|
-
|
26
|
-
|
26
|
+
return if self.has_attribute?(:con_state) == false || self.con_state.nil? || self.con_state == Labimotion::ConState::NONE
|
27
|
+
|
28
|
+
return if attachable_id.nil? && self.con_state != Labimotion::ConState::WAIT
|
29
|
+
|
27
30
|
case con_state
|
28
31
|
when Labimotion::ConState::NMR
|
29
|
-
|
30
|
-
|
31
|
-
self.con_state = Labimotion::ConState::NONE
|
32
|
-
else
|
33
|
-
Labimotion::NmrMapperRepo.process(id, content)
|
34
|
-
self.con_state = Labimotion::ConState::PROCESSED
|
35
|
-
end
|
32
|
+
self.con_state = Labimotion::NmrMapper.process_ds(id)
|
33
|
+
update_column(:con_state, con_state)
|
36
34
|
when Labimotion::ConState::WAIT
|
37
35
|
self.con_state = Labimotion::Converter.jcamp_converter(id)
|
36
|
+
update_column(:con_state, con_state)
|
37
|
+
when Labimotion::ConState::CONVERTED
|
38
|
+
Labimotion::Converter.metadata(id)
|
38
39
|
end
|
39
|
-
update_column(:con_state, con_state)
|
40
40
|
end
|
41
41
|
end
|
42
42
|
end
|
@@ -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 = '1.0.17'
|
7
|
+
VERSION_REPO = '0.3.3'
|
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
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name: labimotion
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3
3
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version: !ruby/object:Gem::Version
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4
|
-
version: 0.3.
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4
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+
version: 0.3.3
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5
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platform: ruby
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6
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authors:
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7
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- Chia-Lin Lin
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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10
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bindir: bin
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cert_chain: []
|
12
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-
date: 2023-
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+
date: 2023-10-19 00:00:00.000000000 Z
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13
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rails
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@@ -34,12 +34,13 @@ extensions: []
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extra_rdoc_files: []
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files:
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36
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- lib/labimotion.rb
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37
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-
- lib/labimotion/api.rb
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38
37
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- lib/labimotion/apis/converter_api.rb
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39
38
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- lib/labimotion/apis/generic_dataset_api.rb
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40
39
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- lib/labimotion/apis/generic_element_api.rb
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40
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- lib/labimotion/apis/labimotion_hub_api.rb
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42
41
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- lib/labimotion/apis/segment_api.rb
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42
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+
- lib/labimotion/collection/export.rb
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43
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+
- lib/labimotion/collection/import.rb
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43
44
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- lib/labimotion/entities/application_entity.rb
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44
45
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- lib/labimotion/entities/dataset_entity.rb
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46
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- lib/labimotion/entities/dataset_klass_entity.rb
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@@ -65,7 +66,6 @@ files:
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- lib/labimotion/libs/converter.rb
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- lib/labimotion/libs/export_dataset.rb
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68
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- lib/labimotion/libs/nmr_mapper.rb
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68
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-
- lib/labimotion/libs/nmr_mapper_repo.rb
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- lib/labimotion/libs/template_hub.rb
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- lib/labimotion/models/collections_element.rb
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- lib/labimotion/models/concerns/attachment_converter.rb
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@@ -90,15 +90,14 @@ files:
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- lib/labimotion/models/segment_klasses_revision.rb
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- lib/labimotion/models/segments_revision.rb
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92
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- lib/labimotion/utils/con_state.rb
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93
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-
- lib/labimotion/utils/
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94
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-
- lib/labimotion/utils/import.rb
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93
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+
- lib/labimotion/utils/import_utils.rb
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94
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- lib/labimotion/utils/search.rb
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95
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- lib/labimotion/utils/serializer.rb
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96
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- lib/labimotion/utils/utils.rb
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97
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- lib/labimotion/version.rb
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99
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-
homepage: https://
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+
homepage: https://gitlab.kit.edu/kit/labimotion/labimotion
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99
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licenses:
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-
-
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+
- GPL-3.0
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metadata: {}
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post_install_message:
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rdoc_options: []
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data/lib/labimotion/api.rb
DELETED
@@ -1,19 +0,0 @@
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1
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# frozen_string_literal: true
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-
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## This is the first version of the dataset class
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module Labimotion
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## This is the first version of the dataset class
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class Api
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def initialize
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# Initialization code
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end
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-
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def gget_data
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'Hello, worlddddddddddddddddddddd!'
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end
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def self.hello
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'Hellooooooooooooooooooooo!'
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end
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end
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end
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@@ -1,278 +0,0 @@
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|
1
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-
# frozen_string_literal: true
|
2
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-
require 'labimotion/version'
|
3
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-
require 'labimotion/utils/utils'
|
4
|
-
|
5
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-
module Labimotion
|
6
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-
class NmrMapperRepo
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7
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-
def self.is_brucker_binary(id)
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-
att = Attachment.find(id)
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9
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-
if Labimotion::IS_RAILS5 == true
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10
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Zip::File.open(att.store.path) do |zip_file|
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zip_file.each do |entry|
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if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
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metadata = entry.get_input_stream.read.force_encoding('UTF-8')
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return metadata
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end
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end
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end
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else
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if att&.attachment_attacher&.file&.url
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Zip::File.open(att.attachment_attacher.file.url) do |zip_file|
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zip_file.each do |entry|
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if entry.name.include?('/pdata/') && entry.name.include?('parm.txt')
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metadata = entry.get_input_stream.read.force_encoding('UTF-8')
|
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|
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return metadata
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end
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-
end
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end
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end
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end
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nil
|
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end
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def self.process(id, content)
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att = Attachment.find(id)
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lines = content.split("\n").reject(&:empty?)
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metadata = {}
|
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lines.map do |ln|
|
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arr = ln.split(/\s+/)
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metadata[arr[0]] = arr[1..-1].join(' ') if arr.length > 1
|
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-
end
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ols = 'CHMO:0000593' if metadata['NUC1'] == '1H'
|
43
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-
ols = 'CHMO:0000595' if metadata['NUC1'] == '13C'
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-
if content.present? && att.present?
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Labimotion::NmrMapper.ts('write', att.attachable_id,
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content: { metadata: metadata, ols: ols })
|
47
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end
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end
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-
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def self.fetch_content(id)
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Labimotion::NmrMapper.ts('read', id)
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end
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-
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54
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def self.generate_ds(id, current_user = {})
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data = Labimotion::NmrMapper.fetch_content(id)
|
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return if data.nil?
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obj = Labimotion::NmrMapper.build_ds(id, data[:content])
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return if obj.nil? || obj[:ols].nil?
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-
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Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000593'
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Labimotion::NmrMapper.update_ds_1h(id, obj, current_user) if obj[:ols] == 'CHMO:0000595'
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Labimotion::NmrMapper.clean(id)
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end
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-
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def self.update_ds_13c(id, obj)
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67
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# dataset = obj[:dataset]
|
68
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# metadata = obj[:metadata]
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69
|
-
# new_prop = dataset.properties
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70
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-
|
71
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# dataset.properties = new_prop
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# dataset.save!
|
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end
|
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-
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75
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def self.set_data(prop, field, idx, layer_name, field_name, value)
|
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return if field['field'] != field_name || value&.empty?
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field['value'] = value
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prop['layers'][layer_name]['fields'][idx] = field
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prop
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end
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83
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def self.update_ds_1h(id, obj, current_user)
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dataset = obj[:dataset]
|
85
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metadata = obj[:metadata]
|
86
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new_prop = dataset.properties
|
87
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new_prop.dig('layers', 'general', 'fields')&.each_with_index do |fi, idx|
|
88
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# new_prop = set_data(new_prop, fi, idx, 'general', 'title', metadata['NAME'])
|
89
|
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if fi['field'] == 'title' && metadata['NAME'].present?
|
90
|
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## fi['label'] = fi['label']
|
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|
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fi['value'] = metadata['NAME']
|
92
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fi['device'] = metadata['NAME']
|
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fi['dkey'] = 'NAME'
|
94
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new_prop['layers']['general']['fields'][idx] = fi
|
95
|
-
end
|
96
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-
|
97
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if fi['field'] == 'date' && metadata['Date_'].present?
|
98
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## fi['label'] = fi['label']
|
99
|
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fi['value'] = metadata['Date_']
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fi['device'] = metadata['Date_']
|
101
|
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fi['dkey'] = 'Date_'
|
102
|
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new_prop['layers']['general']['fields'][idx] = fi
|
103
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-
end
|
104
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-
|
105
|
-
if fi['field'] == 'time' && metadata['Time'].present?
|
106
|
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## fi['label'] = fi['label']
|
107
|
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fi['value'] = metadata['Time']
|
108
|
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fi['device'] = metadata['Time']
|
109
|
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fi['dkey'] = 'Time'
|
110
|
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new_prop['layers']['general']['fields'][idx] = fi
|
111
|
-
end
|
112
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-
|
113
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if fi['field'] == 'creator' && current_user.present?
|
114
|
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## fi['label'] = fi['label']
|
115
|
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fi['value'] = current_user.name
|
116
|
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new_prop['layers']['general']['fields'][idx] = fi
|
117
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-
end
|
118
|
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end
|
119
|
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element = Container.find(id)&.root_element
|
120
|
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element.present? && element&.class&.name == 'Sample' && new_prop.dig('layers', 'sample_details', 'fields')&.each_with_index do |fi, idx|
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if fi['field'] == 'label'
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122
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fi['value'] = element.short_label
|
123
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new_prop['layers']['sample_details']['fields'][idx] = fi
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124
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end
|
125
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if fi['field'] == 'id'
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126
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fi['value'] = element.id
|
127
|
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new_prop['layers']['sample_details']['fields'][idx] = fi
|
128
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end
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129
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end
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130
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-
|
131
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new_prop.dig('layers', 'instrument', 'fields')&.each_with_index do |fi, idx|
|
132
|
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if fi['field'] == 'instrument' && metadata['INSTRUM'].present?
|
133
|
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# fi['label'] = fi['label']
|
134
|
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fi['value'] = metadata['INSTRUM']
|
135
|
-
fi['device'] = metadata['INSTRUM']
|
136
|
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fi['dkey'] = 'INSTRUM'
|
137
|
-
new_prop['layers']['instrument']['fields'][idx] = fi
|
138
|
-
end
|
139
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-
end
|
140
|
-
|
141
|
-
|
142
|
-
new_prop.dig('layers', 'equipment', 'fields')&.each_with_index do |fi, idx|
|
143
|
-
if fi['field'] == 'probehead' && metadata['PROBHD'].present?
|
144
|
-
# fi['label'] = fi['label']
|
145
|
-
fi['value'] = metadata['PROBHD']
|
146
|
-
fi['device'] = metadata['PROBHD']
|
147
|
-
fi['dkey'] = 'PROBHD'
|
148
|
-
new_prop['layers']['equipment']['fields'][idx] = fi
|
149
|
-
end
|
150
|
-
end
|
151
|
-
|
152
|
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new_prop.dig('layers', 'sample_preparation', 'fields')&.each_with_index do |fi, idx|
|
153
|
-
if fi['field'] == 'solvent' && metadata['SOLVENT'].present?
|
154
|
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# fi['label'] = fi['label']
|
155
|
-
fi['value'] = metadata['SOLVENT']
|
156
|
-
fi['device'] = metadata['SOLVENT']
|
157
|
-
fi['dkey'] = 'SOLVENT'
|
158
|
-
fi['value'] = 'chloroform-D1 (CDCl3)' if metadata['SOLVENT'] == 'CDCl3'
|
159
|
-
new_prop['layers']['sample_preparation']['fields'][idx] = fi
|
160
|
-
end
|
161
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-
end
|
162
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-
|
163
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-
|
164
|
-
new_prop.dig('layers', 'set', 'fields')&.each_with_index do |fi, idx|
|
165
|
-
if fi['field'] == 'temperature' && metadata['TE'].present?
|
166
|
-
# fi['label'] = fi['label']
|
167
|
-
fi['value'] = metadata['TE'].split(/\s+/).first
|
168
|
-
fi['device'] = metadata['TE']
|
169
|
-
fi['dkey'] = 'TE'
|
170
|
-
fi['value_system'] = metadata['TE'].split(/\s+/).last
|
171
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
172
|
-
end
|
173
|
-
if fi['field'] == 'ns' && metadata['NS'].present?
|
174
|
-
# fi['label'] = fi['label']
|
175
|
-
fi['value'] = metadata['NS']
|
176
|
-
fi['device'] = metadata['NS']
|
177
|
-
fi['dkey'] = 'NS'
|
178
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
179
|
-
end
|
180
|
-
if fi['field'] == 'PULPROG' && metadata['PULPROG'].present?
|
181
|
-
# fi['label'] = fi['label']
|
182
|
-
fi['value'] = metadata['PULPROG']
|
183
|
-
fi['device'] = metadata['PULPROG']
|
184
|
-
fi['dkey'] = 'PULPROG'
|
185
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
186
|
-
end
|
187
|
-
if fi['field'] == 'td' && metadata['TD'].present?
|
188
|
-
# fi['label'] = fi['label']
|
189
|
-
fi['value'] = metadata['TD']
|
190
|
-
fi['device'] = metadata['TD']
|
191
|
-
fi['dkey'] = 'TD'
|
192
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
193
|
-
end
|
194
|
-
if fi['field'] == 'done' && metadata['D1'].present?
|
195
|
-
# fi['label'] = fi['label']
|
196
|
-
fi['value'] = metadata['D1']
|
197
|
-
fi['device'] = metadata['D1']
|
198
|
-
fi['dkey'] = 'D1'
|
199
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
200
|
-
end
|
201
|
-
if fi['field'] == 'sf' && metadata['SF'].present?
|
202
|
-
## fi['label'] = fi['label']
|
203
|
-
fi['value'] = metadata['SF']
|
204
|
-
fi['device'] = metadata['SF']
|
205
|
-
fi['dkey'] = 'SF'
|
206
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
207
|
-
end
|
208
|
-
if fi['field'] == 'sfoone' && metadata['SFO1'].present?
|
209
|
-
## fi['label'] = fi['label']
|
210
|
-
fi['value'] = metadata['SFO1']
|
211
|
-
fi['device'] = metadata['SFO1']
|
212
|
-
fi['dkey'] = 'SFO1'
|
213
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
214
|
-
end
|
215
|
-
if fi['field'] == 'sfotwo' && metadata['SFO2'].present?
|
216
|
-
## fi['label'] = fi['label']
|
217
|
-
fi['value'] = metadata['SFO2']
|
218
|
-
fi['device'] = metadata['SFO2']
|
219
|
-
fi['dkey'] = 'SFO2'
|
220
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
221
|
-
end
|
222
|
-
if fi['field'] == 'nucone' && metadata['NUC1'].present?
|
223
|
-
## fi['label'] = fi['label']
|
224
|
-
fi['value'] = metadata['NUC1']
|
225
|
-
fi['device'] = metadata['NUC1']
|
226
|
-
fi['dkey'] = 'NUC1'
|
227
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
228
|
-
end
|
229
|
-
if fi['field'] == 'nuctwo' && metadata['NUC2'].present?
|
230
|
-
## fi['label'] = fi['label']
|
231
|
-
fi['value'] = metadata['NUC2']
|
232
|
-
fi['device'] = metadata['NUC2']
|
233
|
-
fi['dkey'] = 'NUC2'
|
234
|
-
new_prop['layers']['set']['fields'][idx] = fi
|
235
|
-
end
|
236
|
-
end
|
237
|
-
dataset.properties = new_prop
|
238
|
-
dataset.save!
|
239
|
-
end
|
240
|
-
|
241
|
-
|
242
|
-
def self.ts(method, identifier, params = nil)
|
243
|
-
Rails.cache.send(method, "#{Labimotion::NmrMapper.new.class.name}#{identifier}", params)end
|
244
|
-
|
245
|
-
def self.clean(id)
|
246
|
-
Labimotion::NmrMapper.ts('delete', id)
|
247
|
-
end
|
248
|
-
|
249
|
-
def self.build_ds(id, content)
|
250
|
-
ds = Container.find_by(id: id)
|
251
|
-
return if ds.nil? || content.nil?
|
252
|
-
|
253
|
-
ols = content[:ols]
|
254
|
-
metadata = content[:metadata]
|
255
|
-
|
256
|
-
return if ols.nil? || metadata.nil?
|
257
|
-
|
258
|
-
klass = Labimotion::DatasetKlass.find_by(ols_term_id: ols)
|
259
|
-
return if klass.nil?
|
260
|
-
|
261
|
-
uuid = SecureRandom.uuid
|
262
|
-
props = klass.properties_release
|
263
|
-
props['uuid'] = uuid
|
264
|
-
props['pkg'] = Labimotion::Utils.pkg(props['pkg'])
|
265
|
-
props['klass'] = 'Dataset'
|
266
|
-
dataset = Labimotion::Dataset.create!(
|
267
|
-
uuid: uuid,
|
268
|
-
dataset_klass_id: klass.id,
|
269
|
-
element_type: 'Container',
|
270
|
-
element_id: ds.id,
|
271
|
-
properties: props,
|
272
|
-
properties_release: klass.properties_release,
|
273
|
-
klass_uuid: klass.uuid
|
274
|
-
)
|
275
|
-
{ dataset: dataset, metadata: metadata, ols: ols }
|
276
|
-
end
|
277
|
-
end
|
278
|
-
end
|