miga-base 1.3.14.7 → 1.3.15.1

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@@ -32,8 +32,8 @@ module MiGA::Cli::Action::Download::Seqcode
32
32
  :seqcode, :'type-genomes', nil, :json, nil, page: current_page
33
33
  )
34
34
  doc = MiGA::Json.parse(json, contents: true)
35
- current_page = doc[:current_page] + 1
36
- total_pages = doc[:total_pages]
35
+ current_page = doc.dig(:response, :current_page) + 1
36
+ total_pages = doc.dig(:response, :total_pages)
37
37
 
38
38
  doc[:values].each do |name|
39
39
  next unless name[:type_material]
@@ -261,10 +261,12 @@ module MiGA::Dataset::Result::Add
261
261
  def add_result_distances_nonref(base)
262
262
  return nil unless
263
263
  result_files_exist?(base, %w[.aai-medoids.tsv .aai.db]) ||
264
- result_files_exist?(base, %w[.ani-medoids.tsv .ani.db])
264
+ result_files_exist?(base, %w[.ani-medoids.tsv .ani.db]) ||
265
+ result_files_exist?(base, %w[.empty])
265
266
 
266
267
  add_files_to_ds_result(
267
268
  MiGA::Result.new("#{base}.json"), name,
269
+ empty: '.empty',
268
270
  aai_medoids: '.aai-medoids.tsv',
269
271
  haai_db: '.haai.db',
270
272
  aai_db: '.aai.db',
@@ -22,7 +22,7 @@ module MiGA::RemoteDataset::Base
22
22
  @@_EUTILS = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
23
23
  @@_EBI_API = 'https://www.ebi.ac.uk/Tools/'
24
24
  @@_GTDB_API = 'https://gtdb-api.ecogenomic.org/'
25
- @@_SEQCODE_API = 'https://disc-genomics.uibk.ac.at/seqcode/'
25
+ @@_SEQCODE_API = 'https://api.seqco.de/v1/'
26
26
  @@_EUTILS_BUILD = lambda { |service, q|
27
27
  q[:api_key] = ENV['NCBI_API_KEY'] if ENV['NCBI_API_KEY']
28
28
  uri_safe_join(@@_EUTILS, "#{service}.fcgi")
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, 14, 7].freeze
15
+ VERSION = [1.3, 15, 1].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, 4, 24)
23
+ VERSION_DATE = Date.new(2024, 5, 6)
24
24
 
25
25
  ##
26
26
  # References of MiGA
@@ -29,44 +29,46 @@ blast=no
29
29
  blat=no
30
30
  diamond=no
31
31
  fastani=no
32
- case $(miga option -P "$PROJECT" -k haai_p) in
33
- fastaai)
34
- fastaai=yes
35
- ;;
36
- diamond)
37
- diamond=yes
38
- aai=yes
39
- ;;
40
- blast)
41
- blast=yes
42
- aai=yes
43
- ;;
44
- esac
32
+ if [[ ! -s "${DATASET}.empty" ]] ; then
33
+ case $(miga option -P "$PROJECT" -k haai_p) in
34
+ fastaai)
35
+ fastaai=yes
36
+ ;;
37
+ diamond)
38
+ diamond=yes
39
+ aai=yes
40
+ ;;
41
+ blast)
42
+ blast=yes
43
+ aai=yes
44
+ ;;
45
+ esac
45
46
 
46
- case $(miga option -P "$PROJECT" -k aai_p) in
47
- diamond)
48
- diamond=yes
49
- aai=yes
50
- ;;
51
- blast)
52
- blast=yes
53
- aai=yes
54
- ;;
55
- esac
47
+ case $(miga option -P "$PROJECT" -k aai_p) in
48
+ diamond)
49
+ diamond=yes
50
+ aai=yes
51
+ ;;
52
+ blast)
53
+ blast=yes
54
+ aai=yes
55
+ ;;
56
+ esac
56
57
 
57
- case $(miga option -P "$PROJECT" -k ani_p) in
58
- blast)
59
- blast=yes
60
- ani=yes
61
- ;;
62
- blat)
63
- blat=yes
64
- ani=yes
65
- ;;
66
- fastani)
67
- fastani=yes
68
- ;;
69
- esac
58
+ case $(miga option -P "$PROJECT" -k ani_p) in
59
+ blast)
60
+ blast=yes
61
+ ani=yes
62
+ ;;
63
+ blat)
64
+ blat=yes
65
+ ani=yes
66
+ ;;
67
+ fastani)
68
+ fastani=yes
69
+ ;;
70
+ esac
71
+ fi
70
72
 
71
73
 
72
74
  miga date > "${DATASET}.done"
@@ -35,7 +35,7 @@ class MiGA::DistanceRunner
35
35
 
36
36
  # Launch the appropriate analysis
37
37
  def go!
38
- $stderr.puts "Launching analysis"
38
+ $stderr.puts 'Launching analysis'
39
39
  return if dataset.multi?
40
40
 
41
41
  Dir.mktmpdir do |tmp_dir|
@@ -68,6 +68,14 @@ class MiGA::DistanceRunner
68
68
  # Launch analysis for query datasets
69
69
  def go_query!
70
70
  $stderr.puts 'Launching analysis for query dataset'
71
+
72
+ # Check if the project is empty
73
+ if ref_project.dataset_ref_active.empty?
74
+ out_base = File.expand_path(dataset.name, home)
75
+ File.open("#{out_base}.empty", 'w') { |fh| fh.puts 'Empty ref_project' }
76
+ return
77
+ end
78
+
71
79
  # Check if project is ready
72
80
  tsk = ref_project.clade? ? [:subclades, :ani] : [:clade_finding, :aai]
73
81
  res = ref_project.result(tsk[0])
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: 1.3.14.7
4
+ version: 1.3.15.1
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: 2024-04-24 00:00:00.000000000 Z
11
+ date: 2024-05-06 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: daemons