Support analyses with empty ref_project

Close #176
bio-miga · May 6, 2024 · 168ee28 · 168ee28
1 parent a71e2a6
commit 168ee28
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Showing 4 changed files with 52 additions and 40 deletions.
diff --git a/lib/miga/dataset/result/add.rb b/lib/miga/dataset/result/add.rb
@@ -261,10 +261,12 @@ def add_result_distances_ref(base)
   def add_result_distances_nonref(base)
     return nil unless
       result_files_exist?(base, %w[.aai-medoids.tsv .aai.db]) ||
-      result_files_exist?(base, %w[.ani-medoids.tsv .ani.db])
+      result_files_exist?(base, %w[.ani-medoids.tsv .ani.db]) ||
+      result_files_exist?(base, %w[.empty])
 
     add_files_to_ds_result(
       MiGA::Result.new("#{base}.json"), name,
+      empty: '.empty',
       aai_medoids: '.aai-medoids.tsv',
       haai_db: '.haai.db',
       aai_db: '.aai.db',

diff --git a/lib/miga/version.rb b/lib/miga/version.rb
@@ -12,15 +12,15 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 15, 0].freeze
+  VERSION = [1.3, 15, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
   VERSION_NAME = 'mezzotint'
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 5, 2)
+  VERSION_DATE = Date.new(2024, 5, 6)
 
   ##
   # References of MiGA

diff --git a/scripts/distances.bash b/scripts/distances.bash
@@ -29,44 +29,46 @@ blast=no
 blat=no
 diamond=no
 fastani=no
-case $(miga option -P "$PROJECT" -k haai_p) in
-  fastaai)
-    fastaai=yes
-    ;;
-  diamond)
-    diamond=yes
-    aai=yes
-    ;;
-  blast)
-    blast=yes
-    aai=yes
-    ;;
-esac
+if [[ ! -s "${DATASET}.empty" ]] ; then
+  case $(miga option -P "$PROJECT" -k haai_p) in
+    fastaai)
+      fastaai=yes
+      ;;
+    diamond)
+      diamond=yes
+      aai=yes
+      ;;
+    blast)
+      blast=yes
+      aai=yes
+      ;;
+  esac
 
-case $(miga option -P "$PROJECT" -k aai_p) in
-  diamond)
-    diamond=yes
-    aai=yes
-    ;;
-  blast)
-    blast=yes
-    aai=yes
-    ;;
-esac
+  case $(miga option -P "$PROJECT" -k aai_p) in
+    diamond)
+      diamond=yes
+      aai=yes
+      ;;
+    blast)
+      blast=yes
+      aai=yes
+      ;;
+  esac
 
-case $(miga option -P "$PROJECT" -k ani_p) in
-  blast)
-    blast=yes
-    ani=yes
-    ;;
-  blat)
-    blat=yes
-    ani=yes
-    ;;
-  fastani)
-    fastani=yes
-    ;;
-esac
+  case $(miga option -P "$PROJECT" -k ani_p) in
+    blast)
+      blast=yes
+      ani=yes
+      ;;
+    blat)
+      blat=yes
+      ani=yes
+      ;;
+    fastani)
+      fastani=yes
+      ;;
+  esac
+fi
 
 
 miga date > "${DATASET}.done"

diff --git a/utils/distance/runner.rb b/utils/distance/runner.rb
@@ -35,7 +35,7 @@ def initialize(project_path, dataset_name, opts_hash = {})
 
   # Launch the appropriate analysis
   def go!
-    $stderr.puts "Launching analysis"
+    $stderr.puts 'Launching analysis'
     return if dataset.multi?
 
     Dir.mktmpdir do |tmp_dir|
@@ -68,6 +68,14 @@ def go_ref!
   # Launch analysis for query datasets
   def go_query!
     $stderr.puts 'Launching analysis for query dataset'
+
+    # Check if the project is empty
+    if ref_project.dataset_ref_active.empty?
+      out_base = File.expand_path(dataset.name, home)
+      File.open("#{out_base}.empty", 'w') { |fh| fh.puts 'Empty ref_project' }
+      return
+    end
+
     # Check if project is ready
     tsk = ref_project.clade? ? [:subclades, :ani] : [:clade_finding, :aai]
     res = ref_project.result(tsk[0])