miga-base 1.2.14.2 → 1.2.15.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b8a1b62d1125f54550d8cf801c46924abb79085005b8fa4abe732e9347b1fa82
-  data.tar.gz: baa4a96d604fd649147f47aafeaea038310b8ec588edb8055f7d511842ba3f6b
+  metadata.gz: 9de962d747353644dddff05181f74c87a3f401df14e81d1810f125c9d1843351
+  data.tar.gz: 3dd90251f07976c36adfdabaa603e399bc046f68c14ff83680eb6a6de4219159
 SHA512:
-  metadata.gz: 1ab3bed5edbd0e9ef513c731c9d28999bdb483547376446746157b58bddc92a9ddde7e0cdfd7766351f11e69f1e11df8e2ccf94815ab95108842caa43f6fdd29
-  data.tar.gz: b3401886ca9139d3ed3a9c19188a1b171254c0d0c1c21d63beffb71b497713dac59ba5fb0176bf2340bc48595640dc6dadfba7881aa7c993cd82894b0679c8a6
+  metadata.gz: 68f3c9616c1d2ad0fed1f03fc6b1054d428fa8b61999febcf6394d34c261550e203b108d2399a43077d95980b6c623e40799e0bf233cfcc130ff5ef97fdc4e47
+  data.tar.gz: e95d549756ad10f86f4abf1761fb763e8ee218ff81d1cf8f6b597c831227482b6e90871800eb38863a8a12ed622b3222385b5f730e3e4103de06aa24753e8a3a

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

@@ -17,6 +17,10 @@ module MiGA::Cli::Action::Download::Base
       '--ignore-until STRING',
       'Ignores all datasets until a name is found (useful for large reruns)'
     ) { |v| cli[:ignore_until] = v }
+    opt.on(
+      '--ignore-removed',
+      'Ignores entries removed from NCBI (by default fails on removed entries)'
+    ) { |v| cli[:ignore_removed] = v }
     cli.opt_flag(
       opt, 'get-metadata',
       'Only download and update metadata for existing datasets', :get_md
@@ -84,7 +88,11 @@ module MiGA::Cli::Action::Download::Base
 
       downloaded += 1
       unless cli[:dry]
-        save_entry(name, body, p)
+        unless save_entry(name, body, p)
+          downloaded -= 1
+          d.pop
+          next
+        end
         p.save! if cli[:save_every] > 1 && (downloaded % cli[:save_every]).zero?
       end
     end
@@ -93,6 +101,9 @@ module MiGA::Cli::Action::Download::Base
     [d, downloaded]
   end
 
+  ##
+  # Saves the (generic remote) entry identified by +name+ with +body+ into the
+  # project +p+, and returns +true+ on success and +false+ otherwise
   def save_entry(name, body, p)
     cli.say '  Locating remote dataset'
     body[:md][:metadata_only] = true if cli[:only_md]
@@ -105,5 +116,9 @@ module MiGA::Cli::Action::Download::Base
       rd.save_to(p, name, !cli[:query], body[:md])
       cli.add_metadata(p.add_dataset(name))
     end
+    true
+  rescue MiGA::RemoteDataMissingError => e
+    raise(e) unless cli[:ignore_removed]
+    false
   end
 end

data/lib/miga/common/errors.rb

@@ -9,4 +9,14 @@ module MiGA
   # An error with a system call
   class SystemCallError < Error
   end
+
+  ##
+  # An error with remote data
+  class RemoteDataError < Error
+  end
+
+  ##
+  # An error caused by missing remote data
+  class RemoteDataMissingError < RemoteDataError
+  end
 end

data/lib/miga/remote_dataset/download.rb

@@ -43,6 +43,12 @@ class MiGA::RemoteDataset
     # +format+: String, passed to download
     def ncbi_asm_rest(opts)
       url_dir = opts[:obj].ncbi_asm_json_doc['ftppath_genbank']
+      if url_dir.nil? || url_dir.empty?
+        raise MiGA::RemoteDataMissingError.new(
+          "Missing ftppath_genbank in NCBI Assembly JSON"
+        )
+      end
+
       url = "#{url_dir}/#{File.basename url_dir}_genomic.fna.gz"
       download(
         :web, :assembly_gz, url,

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.2, 14, 2].freeze
+  VERSION = [1.2, 15, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 1, 16)
+  VERSION_DATE = Date.new(2023, 1, 17)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.14.2
+  version: 1.2.15.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-01-16 00:00:00.000000000 Z
+date: 2023-01-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons