Log when makeblastdb is provided a dir without fastas

bin/sequenceserver

@@ -358,7 +358,9 @@ begin
       end
 
       if make_blast_databases?
-        if SequenceServer.makeblastdb.any_to_format_or_reformat?
+        if SequenceServer.makeblastdb.no_fastas?
+          puts "Couldn't find any FASTA files in #{SequenceServer.config[:database_dir]}."
+        elsif SequenceServer.makeblastdb.any_to_format_or_reformat?
           puts
           puts <<~MSG
           SequenceServer has scanned your databases directory and will now offer
@@ -380,7 +382,7 @@ begin
           print '>> '
           response = STDIN.gets.to_s.strip
           SequenceServer.makeblastdb.run unless response =~ /^[n]$/i
-          else
+        else
           puts "All FASTA files in #{SequenceServer.config[:database_dir]} " \
                'are formatted.'
         end

lib/sequenceserver/makeblastdb.rb

@@ -30,6 +30,10 @@ def any_to_format_or_reformat?
       any_to_format? || any_to_reformat?
     end
 
+    def no_fastas?
+      probably_fastas.empty?
+    end
+
     # Runs makeblastdb on each file in `fastas_to_format` and
     # `fastas_to_reformat`.
     def run
@@ -107,22 +111,32 @@ def fastas_to_reformat
     def fastas_to_format
       return @fastas_to_format if defined?(@fastas_to_format)
 
-      @fastas_to_format = []
+      formatted_fasta_paths = formatted_fastas.map { |f| f[0] }
+      fasta_paths_to_format = probably_fastas - formatted_fasta_paths
+
+      @fastas_to_format = fasta_paths_to_format.map do |path|
+        [
+          path,
+          make_db_title(path),
+          guess_sequence_type_in_fasta(path)
+        ]
+      end
+
+      @fastas_to_format
+    end
+
+    def probably_fastas
+      return @probably_fastas if defined?(@probably_fastas)
+
+      @probably_fastas = []
 
-      # Add a trailing slash to database_dir - Find.find doesn't work as
-      # expected without the trailing slash if database_dir is a symlink
-      # inside a docker container.
       Find.find(database_dir + '/') do |path|
         next if File.directory?(path)
-        next unless probably_fasta?(path)
-        next if formatted_fastas.any? { |f| f[0] == path }
 
-        @fastas_to_format << [path,
-                              make_db_title(path),
-                              guess_sequence_type_in_fasta(path)]
+        @probably_fastas << path if probably_fasta?(path)
       end
 
-      @fastas_to_format
+      @probably_fastas
     end
 
     # Runs `blastdbcmd` to determine formatted FASTA files in the database

spec/makeblastdb_spec.rb

@@ -116,6 +116,21 @@ module SequenceServer
       expect(makeblastdb.send(:multipart_database_name?, sample_name3)).to be_truthy
     end
 
+    describe '#no_fastas?' do
+      it 'returns true if no FASTA files are found' do
+        makeblastdb = SequenceServer::MAKEBLASTDB.new(database_dir_without_parse_seqids)
+        expect(makeblastdb.no_fastas?).to be_truthy
+      end
+
+      it 'returns false if FASTA files are found' do
+        makeblastdb = SequenceServer::MAKEBLASTDB.new(database_dir_unformatted)
+        expect(makeblastdb.no_fastas?).to be_falsey
+
+        makeblastdb = SequenceServer::MAKEBLASTDB.new(database_dir_v4)
+        expect(makeblastdb.no_fastas?).to be_falsey
+      end
+    end
+
     describe '#make_blast_database' do
       context 'duplicate sequence ids' do
         before do