miga-base 1.3.1.0 → 1.3.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: d73a7b2585ba65f467f6648e9ebd49033cd822cfcf4392fa201939b591886743
-  data.tar.gz: 468d835c418fae7bb5b3c90bb357783cbfa8133dfadf2bde5d702d648524e000
+  metadata.gz: 25c05f96857b3d2cbaf122636aa72f2993d89d13be0b90c72373854aa16795e8
+  data.tar.gz: 4ed8eae5248c0f6e7939a7067e1b6f537869e855d1a06af2e33b26d6e2d7b6db
 SHA512:
-  metadata.gz: bef438ae52da81802456e7bfac5d6f1ad4e367d20342f5c2c3fc79f4c05d46a7b4023097570ddd127cc80fe119a2114506aa27472512c1a9dce42fbe638f8d9b
-  data.tar.gz: d8426a5097b0bba3f09c3804dd904dae1cae4d5fe1a364647965d71c0ba25eb9ec9da0315a0e856ca4061dba38db6f4d0a720fcd853a784b94bfd199a15729c0
+  metadata.gz: d309f568c2216b4db3fd4b2c7b891ecc36bc0135bcd6e4b1ecf86ee4f42a5083172d5e01eba2ea6b0d5d785ffc57ddf28ce4053b6be0e2648945d42d2989ef0f
+  data.tar.gz: 89ecc0e521b46217fc670d85648446050ac8eb4ea07608741292e2ffa46c91e4797032bc900f2566c78d6f9175349241195d950564fc296e3bbb326874640665

data/lib/miga/cli/action/download/ncbi.rb

@@ -71,16 +71,13 @@ module MiGA::Cli::Action::Download::Ncbi
     CSV.parse(doc, headers: true).each do |r|
       asm = r['assembly']
       next if asm.nil? || asm.empty? || asm == '-'
-      next unless r['ftp_path_genbank']
 
       rep = remote_row_replicons(r)
       n = remote_row_name(r, rep, asm)
 
       # Register for download
-      fna_url = '%s/%s_genomic.fna.gz' %
-                [r['ftp_path_genbank'], File.basename(r['ftp_path_genbank'])]
       ds[n] = {
-        ids: [fna_url], db: :assembly_gz, universe: :web,
+        ids: [asm], db: :assembly, universe: :ncbi,
         md: {
           type: :genome, ncbi_asm: asm, strain: r['strain']
         }
@@ -123,8 +120,7 @@ module MiGA::Cli::Action::Download::Ncbi
         'matching(tab==["Prokaryotes"] and q=="' \
           "#{cli[:taxon]&.tr('"', "'")}\"",
       fields: 'organism|organism,assembly|assembly,replicons|replicons,' \
-        'level|level,ftp_path_genbank|ftp_path_genbank,' \
-        'release_date|release_date,strain|strain',
+        'level|level,release_date|release_date,strain|strain',
       nolimit: 'on'
     }
     if cli[:reference]

data/lib/miga/project.rb

@@ -128,4 +128,19 @@ class MiGA::Project < MiGA::MiGA
     require 'miga/daemon'
     @daemon ||= MiGA::Daemon.new(self)
   end
+
+  ##
+  # Retrieves the option with name +key+ from the project's metadata,
+  # extending support to relative paths in +:ref_project+ and
+  # +:db_proj_dir+
+  def option_by_metadata(key)
+    case key.to_sym
+    when :ref_project, :db_proj_dir
+      y = metadata[key]
+      y = File.expand_path(y, path) if y && y =~ /^[^\/]/
+      return y
+    end
+
+    super
+  end
 end

data/lib/miga/remote_dataset/download.rb

@@ -49,7 +49,7 @@ class MiGA::RemoteDataset
         )
       end
 
-      url = "#{url_dir}/#{File.basename url_dir}_genomic.fna.gz"
+      url = '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
       download(
         :web, :assembly_gz, url,
         opts[:format], opts[:file], opts[:extra], opts[:obj]
@@ -134,9 +134,8 @@ module MiGA::RemoteDataset::Download
   ##
   # Download data into +file+
   def download(file)
-    self.class.download(
-      universe, db, ids, self.class.UNIVERSE[universe][:dbs][db][:format],
-      file, [], self
-    )
+    format = self.class.UNIVERSE[universe][:dbs][db][:format]
+    # MiGA::MiGA.DEBUG "download: #{universe}, #{db}, #{ids}, #{format}"
+    self.class.download(universe, db, ids, format, file, [], self)
   end
 end

data/lib/miga/remote_dataset.rb

@@ -216,7 +216,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
     end
     return nil unless metadata[:ncbi_asm]
 
-    ncbi_asm_id = self.class.ncbi_asm_acc2id metadata[:ncbi_asm]
+    ncbi_asm_id = self.class.ncbi_asm_acc2id(metadata[:ncbi_asm])
     txt = nil
     3.times do
       txt = self.class.download(:ncbi_summary, :assembly, ncbi_asm_id, :json)
@@ -226,6 +226,12 @@ class MiGA::RemoteDataset < MiGA::MiGA
     return if doc.nil? || doc['result'].nil? || doc['result'].empty?
 
     @_ncbi_asm_json_doc = doc['result'][ doc['result']['uids'].first ]
+    url_dir = @_ncbi_asm_json_doc['ftppath_genbank']
+    if url_dir
+      metadata[:web_assembly_gz] ||=
+        '%s/%s_genomic.fna.gz' % [url_dir, File.basename(url_dir)]
+    end
+    @_ncbi_asm_json_doc
   end
 
   private

data/lib/miga/version.rb

@@ -12,15 +12,15 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 1, 0].freeze
+  VERSION = [1.3, 3, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
-  VERSION_NAME = 'prima'
+  VERSION_NAME = 'mezzotint'
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 3, 21)
+  VERSION_DATE = Date.new(2023, 3, 29)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.1.0
+  version: 1.3.3.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-03-21 00:00:00.000000000 Z
+date: 2023-03-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons