miga-base 1.3.21.0 → 1.3.21.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 27c260214690d23cf63214ecbd8bab0671af2450bf0edd6f4fabfb17b9a8c71c
-  data.tar.gz: ce22d314727280fc4c0c8707ac8e4997361a611d3134321cb9de35bf9455fdab
+  metadata.gz: 8cdfd44decfe646a4acbda6c5f4569189d1d647c396a39688a9bf2468766fd30
+  data.tar.gz: 5a61d4f447a4695f90028d4b55604ff36585afa156cb7cd6910e2d23a6488efc
 SHA512:
-  metadata.gz: 76d0b214b27547b22118557c0f733649b7f73c5bd3c6fe67c09a84f4fac5b232b79011de5c11e9cd90656db796eb84c59ac6b553e90f8e2f8ffb7f9be8feba34
-  data.tar.gz: d4eaf235af72b9b168660f0b518f7ffbfa6fc58f3b92acf4c9f99c469cd786de71b68569c859a549f5f49ae32e17737edbf0be80619ed5ba19ce4b1a3daa1569
+  metadata.gz: c7faf6742be1fe0bed5606e2c0ef28c96e98a2b31ade5a613e6b2f2feac3d224b0b6ae40664c82963750d26e8287b98a3220d5ada50d5e396b88c4a51554ccab
+  data.tar.gz: 88055ad7f63d14f525cbd079a125de9a6f3373bb7ab3bb1e51a81248db1bc88272807b87706aafe5aeca27222a48cf9e6794037cbba631cd5747bee644b1b7a8

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

@@ -16,6 +16,7 @@ class MiGA::Cli::Action::Lair < MiGA::Cli::Action
         run: 'Start the application and stay on top',
         status: 'Show status (PID) of application instances',
         list: 'List all daemons and their status',
+        running: 'List running daemons only',
         terminate: 'Terminate all daemons in the lair and exit'
       }.each { |k, v| opt.separator sprintf('    %*s%s', -33, k, v) }
       opt.separator ''
@@ -93,12 +94,17 @@ class MiGA::Cli::Action::Lair < MiGA::Cli::Action
     case cli.operation.to_sym
     when :terminate
       lair.terminate_daemons
-    when :list
+    when :list, :running
       o = []
       lair.each_daemon do |d|
         o << [d.daemon_name, d.class, d.daemon_home, d.active?, d.last_alive]
       end
-      cli.table(%w[name class path active last_alive], o)
+      if cli.operation.to_sym == :running
+        o.select! { |i| i[3] }.map! { |i| i[0..-3] }
+        cli.table(%w[name class path], o)
+      else
+        cli.table(%w[name class path active last_alive], o)
+      end
     else
       lair.daemon(cli.operation, cli[:daemon_opts])
     end

data/lib/miga/project.rb

@@ -143,8 +143,8 @@ class MiGA::Project < MiGA::MiGA
   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 =~ /^[^\/]/
+      y = metadata[key] or return
+      y = File.expand_path(y, path)
       return y
     end
 

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, 21, 0].freeze
+  VERSION = [1.3, 21, 2].freeze
 
   ##
   # Nickname for the current major.minor version.

data/scripts/distances.bash

@@ -22,6 +22,7 @@ fi
 ruby -I "$MIGA/lib" "$MIGA/utils/distances.rb" "$PROJECT" "$DATASET"
 
 # Finalize
+refproject=no
 fastaai=no
 aai=no
 ani=no
@@ -29,6 +30,10 @@ blast=no
 blat=no
 diamond=no
 fastani=no
+REF_PROJECT=$(miga option -P "$PROJECT" -D "$DATASET" -k db_project)
+
+[[ -d "$REF_PROJECT" ]] && refproject=yes
+
 if [[ ! -s "${DATASET}.empty" ]] ; then
   case $(miga option -P "$PROJECT" -k haai_p) in
     fastaai)
@@ -76,6 +81,14 @@ cat <<VERSIONS \
   | miga add_result -P "$PROJECT" -D "$DATASET" -r "$SCRIPT" -f --stdin-versions
 => MiGA
 $(miga --version)
+$(
+  if [[ "$refproject" == "yes" ]] ; then
+    echo "=> Reference Project"
+    miga about -P "$REF_PROJECT" -m name
+    echo "=> Reference Project Release"
+    miga about -P "$REF_PROJECT" -m release
+  fi
+)
 $(
   if [[ "$fastaai" == "yes" ]] ; then
     echo "=> FastAAI"

data/scripts/taxonomy.bash

@@ -25,6 +25,7 @@ blat=no
 diamond=no
 fastani=no
 REF_PROJECT=$(miga option -P "$PROJECT" -k ref_project)
+
 if [[ -d "$REF_PROJECT" ]] ; then
   refproject=yes
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.21.0
+  version: 1.3.21.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R