From cb7bd02c50095b9d62bd9ba3a4c6223c91f8c590 Mon Sep 17 00:00:00 2001
From: "Luis M. Rodriguez-R" <lmrodriguezr@gmail.com>
Date: Sat, 28 Sep 2024 11:58:18 +0200
Subject: [PATCH] Add reference project to `distances` versions

---
 lib/miga/project.rb    |  4 ++--
 lib/miga/version.rb    |  2 +-
 scripts/distances.bash | 13 +++++++++++++
 scripts/taxonomy.bash  |  1 +
 4 files changed, 17 insertions(+), 3 deletions(-)

diff --git a/lib/miga/project.rb b/lib/miga/project.rb
index 7a7deb0..e6503bb 100644
--- a/lib/miga/project.rb
+++ b/lib/miga/project.rb
@@ -143,8 +143,8 @@ def daemon
   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
 
diff --git a/lib/miga/version.rb b/lib/miga/version.rb
index 409a8d4..da0a372 100644
--- a/lib/miga/version.rb
+++ b/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, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
diff --git a/scripts/distances.bash b/scripts/distances.bash
index 0ad01d8..1cf0bea 100755
--- a/scripts/distances.bash
+++ b/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"
diff --git a/scripts/taxonomy.bash b/scripts/taxonomy.bash
index b7be7bf..dffeec8 100755
--- a/scripts/taxonomy.bash
+++ b/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