miga-base 1.3.15.12 → 1.3.17.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 445777ed090342dc2c61db44580712ab1a29efb3f54fe66715c7b76ed62a3310
-  data.tar.gz: 78f5fe723814ca20585003ed866031be338fcc5d918c0abca996588ec911af67
+  metadata.gz: e33b9da20704a768d31e9b826676bdcb637a7636ec434fdef4af7eb653744f35
+  data.tar.gz: 28970fcb3723a6304c11d834f8861b37ede641fba77ddd9a2d4950b608fcb6a0
 SHA512:
-  metadata.gz: 56eee3874cd9f7f2f8acdec2b1da0e10bb354201259721e73c0c24f3da1499830f901bee35f03d5313290f39ff27db7a3aa64f5b0454c267be9c455b949d8f8e
-  data.tar.gz: f92b9699f7372cb493cb17ee32d66dbd6751b129de2023092c6e48f9a132a3f8370c7c010fae65bf1703904b3f654d27e106921a786cd5a975979d9607ed811e
+  metadata.gz: 9ff04d00d7e1d4af7b007bbf27e59b35a57678715cf89651befcab48deec95389e1c3ffb330bfae62cd8720bde752f36a9f513f37e410d1ab60158381de700f7
+  data.tar.gz: 33c6aaa9c088b8bfed16c1ffd765fe36d4b797bd01d4145cda989e50faf2dea4ffe93d632cde163fef1e64d4493fc9f164b85770337439c75f59d6a652b89feb

data/lib/miga/cli/action/doctor/operations.rb

@@ -65,6 +65,24 @@ module MiGA::Cli::Action::Doctor::Operations
     cli.say
   end
 
+  ##
+  # Perform md-files operation with MiGA::Cli +cli+
+  def check_mdfiles(cli)
+    cli.say 'Looking for unregistered files in the metadata folder'
+    md = File.join(cli.load_project.path, 'metadata')
+    Dir.each_child(md) do |file|
+      expected_ds = File.basename(file, '.json')
+      next if cli.load_project.dataset_names.include?(expected_ds)
+      file_path = File.join(md, file)
+      if Dir.exist?(file_path)
+        cli.say "  > Ignoring directory: #{file}"
+      else
+        cli.say "  > Removing: #{file}"
+        File.unlink(File.join(md, file))
+      end
+    end
+  end
+
   ##
   # Perform cds operation with MiGA::Cli +cli+
   def check_cds(cli)

data/lib/miga/cli/action/doctor.rb

@@ -49,6 +49,7 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     # TODO Implement this check:
     # refdb:  ['ref-db', 'Check index format of reference databases'],
     status: ['status', 'Update metadata status of all datasets'],
+    mdfiles:['md-files', 'Remove unregistered files in metadata'],
     db:     ['databases', 'Check integrity of database files'],
     dist:   ['distances', 'Check distance summary tables'],
     bidir:  ['bidirectional', 'Check distances are bidirectional'],

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 = [1.3, 15, 12].freeze
+  VERSION = [1.3, 17, 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(2024, 6, 23)
+  VERSION_DATE = Date.new(2024, 6, 28)
 
   ##
   # References of MiGA

data/scripts/ssu.bash

@@ -46,16 +46,17 @@ if [[ -s $fa ]] ; then
       >> "${DATASET}.rdp.tsv"
   fi
 
-  # tRNAscan-SE
-  dom_opt="-$(echo "$d" | perl -pe 's/(\S).*/$1/')"
-  out="${DATASET}.trna.txt"
-  # `echo O` is to avoid a hang from a pre-existing output file.
-  # This is better than pre-checking (and removing), because it avoids
-  # the (unlikely) scenario of a file racing (e.g., a file created right
-  # before tRNAscan-SE starts, or a `rm` failure).
-  #
-  # The trailing `|| true` is to treat failure as non-fatal
-  echo O | tRNAscan-SE $dom_opt -o "${DATASET}.trna.txt" -q "$fa" || true
+  # tRNAscan-SE (only if non-multi)
+  if miga ls -P "$PROJECT" -D "$DATASET" --no-multi --silent ; then
+    dom_opt="-$(echo "$d" | perl -pe 's/(\S).*/$1/')"
+    # `echo O` is to avoid a hang from a pre-existing output file.
+    # This is better than pre-checking (and removing), because it avoids
+    # the (unlikely) scenario of a file racing (e.g., a file created right
+    # before tRNAscan-SE starts, or a `rm` failure).
+    #
+    # The trailing `|| true` is to treat failure as non-fatal
+    echo O | tRNAscan-SE $dom_opt -o "${DATASET}.trna.txt" -q "$fa" || true
+  fi
 
   # Gzip
   for x in gff ssu.all.fa rdp.tsv trna.txt ; do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.15.12
+  version: 1.3.17.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-06-23 00:00:00.000000000 Z
+date: 2024-06-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons