miga-base 1.2.15.4 → 1.2.16.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/miga/cli/action/download/ncbi.rb +15 -3
- data/lib/miga/cli/action/ncbi_get.rb +6 -0
- data/lib/miga/version.rb +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA256:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: '0215026559d070f36a5eacddecaa2a2c4c4717f6506add25b76f1988dfb86483'
|
|
4
|
+
data.tar.gz: 944b5ba3f76e75a988932963db73ab23795f0a266233f555e5617f875aad1d53
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 70b1fb8640127febebf776f80faf75d59b25ab145152ad5d49d78b9a408e5e653cf874bb9e5c5c0749ae4bb790b46ffe9eff504ac646df5c558b72f4ba155be0
|
|
7
|
+
data.tar.gz: ca8d6a4f389b721b4240f70b0da6d02ea8f70c52d0e09b5622d168745a1f082a6fc0b5c5a4d92e2b85844d42bb17e682a52cbd788a0664496c2814c958ce6b7a
|
|
@@ -52,10 +52,22 @@ module MiGA::Cli::Action::Download::Ncbi
|
|
|
52
52
|
end
|
|
53
53
|
|
|
54
54
|
def remote_list
|
|
55
|
-
|
|
55
|
+
doc =
|
|
56
|
+
if cli[:ncbi_table_file]
|
|
57
|
+
cli.say 'Reading genome list from file'
|
|
58
|
+
File.open(cli[:ncbi_table_file], 'r')
|
|
59
|
+
else
|
|
60
|
+
cli.say 'Downloading genome list'
|
|
61
|
+
url = remote_list_url
|
|
62
|
+
MiGA::RemoteDataset.download_url(url)
|
|
63
|
+
end
|
|
64
|
+
ds = parse_csv_as_datasets(doc)
|
|
65
|
+
doc.close if cli[:ncbi_table_file]
|
|
66
|
+
ds
|
|
67
|
+
end
|
|
68
|
+
|
|
69
|
+
def parse_csv_as_datasets(doc)
|
|
56
70
|
ds = {}
|
|
57
|
-
url = remote_list_url
|
|
58
|
-
doc = MiGA::RemoteDataset.download_url(url)
|
|
59
71
|
CSV.parse(doc, headers: true).each do |r|
|
|
60
72
|
asm = r['assembly']
|
|
61
73
|
next if asm.nil? || asm.empty? || asm == '-'
|
|
@@ -29,6 +29,12 @@ class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
|
|
|
29
29
|
'--api-key STRING',
|
|
30
30
|
'::HIDE::' # For backwards compatibility
|
|
31
31
|
) { |v| ENV['NCBI_API_KEY'] = v }
|
|
32
|
+
opt.on(
|
|
33
|
+
'--ncbi-table-file STRING',
|
|
34
|
+
'::HIDE::' # Only meant for debugging
|
|
35
|
+
# It can take the table returned by NCBI and parse it from a file
|
|
36
|
+
# instead of downloading it directly
|
|
37
|
+
) { |v| cli[:ncbi_table_file] = v }
|
|
32
38
|
opt.on(
|
|
33
39
|
'--ncbi-api-key STRING',
|
|
34
40
|
'NCBI API key'
|
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 = [1.2,
|
|
15
|
+
VERSION = [1.2, 16, 0].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(2023, 2,
|
|
23
|
+
VERSION_DATE = Date.new(2023, 2, 8)
|
|
24
24
|
|
|
25
25
|
##
|
|
26
26
|
# References of MiGA
|
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: 1.2.
|
|
4
|
+
version: 1.2.16.0
|
|
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: 2023-02-
|
|
11
|
+
date: 2023-02-08 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: daemons
|