miga-base 1.3.1.0 → 1.3.2.0
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- checksums.yaml +4 -4
- data/lib/miga/cli/action/download/ncbi.rb +2 -6
- data/lib/miga/remote_dataset/download.rb +4 -5
- data/lib/miga/remote_dataset.rb +7 -1
- data/lib/miga/version.rb +3 -3
- metadata +2 -2
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: fa65b4beabfda49a2923c4e7e2cdfe9a8c247c014a2245e5dbdeaa242ff51fa3
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4
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+
data.tar.gz: f29bb637d704a198aaa84760ce1f6b61902b2962f696f43c91c778b5ae87ff67
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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: 53170a680037ad5739d10cf3359df7b1b4e3fb2c2d648065125caa2625116c37575a4e1258bde694529dbc0fedb677776944a18f1fcbf4a42f6c672db7cd3e0a
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7
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+
data.tar.gz: f689dee7de7007686a80e81e7ccdd8f25f270be8172c9b7b627f64bd2788bc926dbc8a00645a0c6f913c8dba40989f33084bab3410efef140a80480c2c020c66
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@@ -71,16 +71,13 @@ module MiGA::Cli::Action::Download::Ncbi
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71
71
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CSV.parse(doc, headers: true).each do |r|
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72
72
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asm = r['assembly']
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73
73
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next if asm.nil? || asm.empty? || asm == '-'
|
74
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-
next unless r['ftp_path_genbank']
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75
74
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76
75
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rep = remote_row_replicons(r)
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77
76
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n = remote_row_name(r, rep, asm)
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78
77
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79
78
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# Register for download
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80
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-
fna_url = '%s/%s_genomic.fna.gz' %
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81
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-
[r['ftp_path_genbank'], File.basename(r['ftp_path_genbank'])]
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82
79
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ds[n] = {
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83
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-
ids: [
|
80
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+
ids: [asm], db: :assembly, universe: :ncbi,
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84
81
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md: {
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85
82
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type: :genome, ncbi_asm: asm, strain: r['strain']
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86
83
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}
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@@ -123,8 +120,7 @@ module MiGA::Cli::Action::Download::Ncbi
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123
120
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'matching(tab==["Prokaryotes"] and q=="' \
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124
121
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"#{cli[:taxon]&.tr('"', "'")}\"",
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125
122
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fields: 'organism|organism,assembly|assembly,replicons|replicons,' \
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126
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-
'level|level,
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127
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-
'release_date|release_date,strain|strain',
|
123
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+
'level|level,release_date|release_date,strain|strain',
|
128
124
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nolimit: 'on'
|
129
125
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}
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130
126
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if cli[:reference]
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@@ -49,7 +49,7 @@ class MiGA::RemoteDataset
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49
49
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)
|
50
50
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end
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51
51
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|
52
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-
url =
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52
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+
url = '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
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53
53
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download(
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54
54
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:web, :assembly_gz, url,
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55
55
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opts[:format], opts[:file], opts[:extra], opts[:obj]
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@@ -134,9 +134,8 @@ module MiGA::RemoteDataset::Download
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134
134
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##
|
135
135
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# Download data into +file+
|
136
136
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def download(file)
|
137
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-
self.class.
|
138
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-
|
139
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-
|
140
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-
)
|
137
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+
format = self.class.UNIVERSE[universe][:dbs][db][:format]
|
138
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+
# MiGA::MiGA.DEBUG "download: #{universe}, #{db}, #{ids}, #{format}"
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139
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+
self.class.download(universe, db, ids, format, file, [], self)
|
141
140
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end
|
142
141
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end
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data/lib/miga/remote_dataset.rb
CHANGED
@@ -216,7 +216,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
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216
216
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end
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217
217
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return nil unless metadata[:ncbi_asm]
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218
218
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|
219
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-
ncbi_asm_id = self.class.ncbi_asm_acc2id
|
219
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+
ncbi_asm_id = self.class.ncbi_asm_acc2id(metadata[:ncbi_asm])
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220
220
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txt = nil
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221
221
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3.times do
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222
222
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txt = self.class.download(:ncbi_summary, :assembly, ncbi_asm_id, :json)
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@@ -226,6 +226,12 @@ class MiGA::RemoteDataset < MiGA::MiGA
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226
226
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return if doc.nil? || doc['result'].nil? || doc['result'].empty?
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227
227
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|
228
228
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@_ncbi_asm_json_doc = doc['result'][ doc['result']['uids'].first ]
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229
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+
url_dir = @_ncbi_asm_json_doc['ftppath_genbank']
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230
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+
if url_dir
|
231
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+
metadata[:web_assembly_gz] ||=
|
232
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+
'%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
|
233
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+
end
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234
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+
@_ncbi_asm_json_doc
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229
235
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end
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230
236
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231
237
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private
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data/lib/miga/version.rb
CHANGED
@@ -12,15 +12,15 @@ module MiGA
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12
12
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# - String indicating release status:
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13
13
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# - rc* release candidate, not released as gem
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14
14
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# - [0-9]+ stable release, released as gem
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15
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-
VERSION = [1.3,
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15
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+
VERSION = [1.3, 2, 0].freeze
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16
16
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17
17
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##
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18
18
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# Nickname for the current major.minor version.
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19
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-
VERSION_NAME = '
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19
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+
VERSION_NAME = 'mezzotint'
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20
20
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|
21
21
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##
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22
22
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# Date of the current gem relese.
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23
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-
VERSION_DATE = Date.new(2023, 3,
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23
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+
VERSION_DATE = Date.new(2023, 3, 25)
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24
24
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25
25
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##
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26
26
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# References of MiGA
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: miga-base
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3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 1.3.
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4
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+
version: 1.3.2.0
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Luis M. Rodriguez-R
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8
8
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autorequire:
|
9
9
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bindir: bin
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10
10
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cert_chain: []
|
11
|
-
date: 2023-03-
|
11
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+
date: 2023-03-25 00:00:00.000000000 Z
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12
12
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dependencies:
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13
13
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- !ruby/object:Gem::Dependency
|
14
14
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name: daemons
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