From a3635c4010f77f2404bb47c4b690a1409aed99e4 Mon Sep 17 00:00:00 2001
From: "Luis M. Rodriguez-R" <lmrodriguezr@gmail.com>
Date: Sat, 28 Sep 2024 11:51:27 +0200
Subject: [PATCH] Centralize handling of `db_project`

---
 lib/miga/dataset.rb      | 15 +++++++++++++++
 lib/miga/version.rb      |  4 ++--
 manual/part5/metadata.md | 15 +++++++++------
 utils/distance/runner.rb |  4 +---
 4 files changed, 27 insertions(+), 11 deletions(-)

diff --git a/lib/miga/dataset.rb b/lib/miga/dataset.rb
index 70b6e20..443bcc4 100644
--- a/lib/miga/dataset.rb
+++ b/lib/miga/dataset.rb
@@ -196,4 +196,19 @@ def closest_relatives(how_many = 1, ref_project = false, metric = :aai)
       [name, how_many]
     )
   end
+
+  ##
+  # Retrieves the option with name +key+ from the dataset's metadata
+  # extending support to relative paths in +:db_project+
+  def option_by_metadata(key)
+    case key.to_sym
+    when :db_project
+      y = metadata[key] or return
+      ref_location = project.option(:db_proj_dir) || File.dirname(project.path)
+      y = File.expand_path(y, ref_location)
+      return y
+    end
+
+    super
+  end
 end
diff --git a/lib/miga/version.rb b/lib/miga/version.rb
index b98e4ec..409a8d4 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, 20, 11].freeze
+  VERSION = [1.3, 21, 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, 9, 13)
+  VERSION_DATE = Date.new(2024, 9, 28)
 
   ##
   # References of MiGA
diff --git a/manual/part5/metadata.md b/manual/part5/metadata.md
index 79794f9..257bb2a 100644
--- a/manual/part5/metadata.md
+++ b/manual/part5/metadata.md
@@ -67,15 +67,15 @@ Metadata entries that trigger specific behaviors in MiGA:
 | min_qual     | Float (or 'no')  | Min. genome quality (or no filter; def: 25)
 | distances_checkpoint | Integer  | Comparisons before storing data (def: 10)
 
-> **{1}** This path can be either absolute or relative to the project's path.
+> **{1}** This path can either be absolute or relative to the project's path
 >
 > **{2}** This is the location of the databases used by
 > [db_project](#dataset-flags). If not set, it is assumed to be the parent
-> folder of the current project.
+> folder of the current project
 >
 > **{3}** Supported values: `blast`, `blat`, `diamond`
 > (only for hAAI and AAI), `fastani` (only for ANI), `no` (only for hAAI),
-> and `fastaai` (only for hAAI).
+> and `fastaai` (only for hAAI)
 >
 > **{4}** One of: `dupont_2012` (default), or `lee_2019`
 
@@ -176,10 +176,13 @@ Metadata entries that trigger specific behaviors in MiGA:
 | Field        | Supported values | Description
 | ------------:|:----------------:|:----------------------------------
 | run_`step`   | Boolean          | Forces running or not `step`
-| db_project   | Path             | Project to use as database
-| dist_req     | Array of String  | Run distances against these datasets*
+| db_project   | Path             | Project to use as database {1}
+| dist_req     | Array of String  | Run distances against these datasets {2}
 
-> **\*** When searching best-matching datasets, include these datasets even if
+> **{1}** By default, it uses its own project as database. The path can be
+> absolute or relative to the parent folder of the project
+> 
+> **{2}** When searching best-matching datasets, include these datasets even if
 > they are not visited using the medoid tree
 
 
diff --git a/utils/distance/runner.rb b/utils/distance/runner.rb
index 18dda0b..8e48390 100644
--- a/utils/distance/runner.rb
+++ b/utils/distance/runner.rb
@@ -19,9 +19,7 @@ def initialize(project_path, dataset_name, opts_hash = {})
       @ref_project = MiGA::Project.load(ref_path)
       raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
     elsif !opts[:run_taxonomy] && dataset.option(:db_project)
-      ref_location = project.option(:db_proj_dir) || File.dirname(project.path)
-      ref_path = File.expand_path(dataset.option(:db_project), ref_location)
-      @ref_project = MiGA::Project.load(ref_path)
+      @ref_project = MiGA::Project.load(dataset.option(:db_project))
       raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
     else
       @ref_project = project