miga-base 1.3.13.0 → 1.3.13.2

Sign up to get free protection for your applications and to get access to all the features.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
1
1
  ---
2
2
  SHA256:
3
- metadata.gz: 8659bae6ee7d40a76a464840a56b4aff77f9a848d777349e98d8c316717b0021
4
- data.tar.gz: dab1cbd8ee24503b4dfbe0e8b034da195120251c258c798bbba92668a52d3cfa
3
+ metadata.gz: 7452e6019471294f9f1b21ef675ff65a4b582eb51df3f0d59c4ee8a084f79540
4
+ data.tar.gz: 1fb9ba522229fa36265c9f5b261c57c44f98e0d31275acd7903c0e4e79f9791a
5
5
  SHA512:
6
- metadata.gz: '09a916e1db7bb4912111e83c2d832a779a245c8eb326aee3cfcead8611d484f737a1cbcae1a1279a2673a2f31a8252c859b533b7ae9b6c74c8881b41e63e7c40'
7
- data.tar.gz: 43e7065632d2642abb0c6bb5fac8ae96e0696c0f48b128376fa5d1ac929c1c7b787df61af78bee5a4824049da7b2baf976f9bb3d3f083184ca02deefc166114e
6
+ metadata.gz: 6519c3bdcf8ce9bfb252a023f9a0dc19ab6534e44f21e8db3199148ae7c2d9588848e18739111b6d444287cf0c6e383ace2b75f77de5bef5da55ea7b7979450e
7
+ data.tar.gz: cb8b25241a73c301c8ceef0c2e08286348047df7a47576a46687444c89d7716f057c87cb5bfa9ed9016a44bcc63aeb5ed96cac1bb46442fe3b574a9923254b69
@@ -186,15 +186,21 @@ class MiGA::RemoteDataset
186
186
  # Looks for the entry +id+ in +dbfrom+, and returns the linked
187
187
  # identifier in +db+ (or nil).
188
188
  def ncbi_map(id, dbfrom, db)
189
+ attempts = 0
189
190
  doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
190
191
  return if doc.empty?
191
192
 
192
- tree = MiGA::Json.parse(doc, contents: true)
193
- [:linksets, 0, :linksetdbs, 0, :links, 0].each do |i|
194
- tree = tree[i]
195
- break if tree.nil?
193
+ begin
194
+ tree = MiGA::Json.parse(doc, contents: true)
195
+ rescue => e
196
+ sleep 5 # <- Usually caused by busy servers: BLOB ID IS NOT IMPLEMENTED
197
+ DEBUG "RETRYING after: #{e}"
198
+ doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
199
+ return if doc.empty?
200
+ tree = MiGA::Json.parse(doc, contents: true)
196
201
  end
197
- tree
202
+
203
+ tree&.dig(:linksets, 0, :linksetdbs, 0, :links, 0)
198
204
  end
199
205
 
200
206
  ##
data/lib/miga/version.rb CHANGED
@@ -12,7 +12,7 @@ module MiGA
12
12
  # - String indicating release status:
13
13
  # - rc* release candidate, not released as gem
14
14
  # - [0-9]+ stable release, released as gem
15
- VERSION = [1.3, 13, 0].freeze
15
+ VERSION = [1.3, 13, 2].freeze
16
16
 
17
17
  ##
18
18
  # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
20
20
 
21
21
  ##
22
22
  # Date of the current gem relese.
23
- VERSION_DATE = Date.new(2024, 3, 10)
23
+ VERSION_DATE = Date.new(2024, 3, 15)
24
24
 
25
25
  ##
26
26
  # References of MiGA
@@ -27,7 +27,7 @@ module MiGA::DistanceRunner::Commands
27
27
  # Launch comparisons
28
28
  pending_targets(targets, :aai).each do |target|
29
29
  # Full AAI
30
- target_cds = target.result(:cds).file_path(:proteins) or next
30
+ target_cds = target.result(:cds)&.file_path(:proteins) or next
31
31
  aairb_cmd(
32
32
  tmp_file('proteins.fa'), target_cds,
33
33
  dataset.name, target.name, tmp_dbs[:aai], checkpoint: :aai
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.3.13.0
4
+ version: 1.3.13.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Luis M. Rodriguez-R
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2024-03-10 00:00:00.000000000 Z
11
+ date: 2024-03-15 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: daemons