Fail gracefully if BLAST+ database(s) is corrupt or has incorrect per…

…mission.

see #145

Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>

bin/sequenceserver

@@ -137,7 +137,8 @@ BANNER
       # error scenarios either when creating a new SequenceServer (first
       # time or later), or updating config values using -s CLI option.
 
-      rescue SequenceServer::CONFIG_FILE_ERROR => e
+      rescue SequenceServer::CONFIG_FILE_ERROR,
+             SequenceServer::BLAST_DATABASE_ERROR => e
 
         puts e
         exit!

lib/sequenceserver.rb

@@ -128,9 +128,7 @@ def init_database
         fail DATABASE_DIR_NOT_FOUND, config[:database_dir]
       end
 
-      assert_blast_databases_present_in_database_dir
       logger.debug("Will use BLAST+ databases at: #{config[:database_dir]}")
-
       Database.scan_databases_dir
       Database.each do |database|
         logger.debug("Found #{database.type} database '#{database.title}'" \
@@ -187,15 +185,6 @@ def assert_blast_installed_and_compatible
       fail BLAST_NOT_COMPATIBLE, version unless version >= MINIMUM_BLAST_VERSION
     end
 
-    def assert_blast_databases_present_in_database_dir
-      cmd = "blastdbcmd -recursive -list #{config[:database_dir]}"
-      out = `#{cmd}`
-      errpat = /BLAST Database error/
-      fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty?
-      fail BLAST_DATABASE_ERROR, cmd, out if out.match(errpat) ||
-                                             !$CHILD_STATUS.success?
-    end
-
     def open_default_browser(url)
       return if using_ssh? || verbose?
       if RUBY_PLATFORM =~ /linux/ && xdg?

lib/sequenceserver/database.rb

@@ -1,4 +1,5 @@
 require 'find'
+require 'open3'
 require 'digest/md5'
 require 'forwardable'
 
@@ -96,17 +97,27 @@ def clear
 
       # Recurisvely scan `database_dir` for blast databases.
       def scan_databases_dir
-        database_dir = config[:database_dir]
-        cmd = "blastdbcmd -recursive -list #{database_dir}" \
-              ' -list_outfmt "%f	%t	%p	%n	%l	%d" 2>&1'
-        list = `#{cmd}`
-        list.each_line do |line|
-          name = line.split('	')[0]
-          next if multipart_database_name?(name)
-          self << Database.new(*line.split('	'))
+        cmd = "blastdbcmd -recursive -list #{config[:database_dir]}" \
+              ' -list_outfmt "%f	%t	%p	%n	%l	%d"'
+        Open3.popen3(cmd) do |_, out, err|
+          out = out.read
+          err = err.read
+          throw_scan_error(cmd, out, err, $CHILD_STATUS)
+          out.each_line do |line|
+            name = line.split('	')[0]
+            next if multipart_database_name?(name)
+            self << Database.new(*line.split('	'))
+          end
         end
       end
 
+      def throw_scan_error(cmd, out, err, child_status)
+        errpat = /BLAST Database error/
+        fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if out.empty?
+        fail BLAST_DATABASE_ERROR.new(cmd, err) if !child_status.success? ||
+                                                   err.match(errpat)
+      end
+
       # Recursively scan `database_dir` for un-formatted FASTA and format them
       # for use with BLAST+.
       def make_blast_databases

lib/sequenceserver/exceptions.rb

@@ -140,7 +140,7 @@ def to_s
   end
 
   # Raised if there was an error determining BLAST+ databases in database_dir.
-  class BLAST_DATABASE_ERROR
+  class BLAST_DATABASE_ERROR < StandardError
     def initialize(cmd, out)
       @cmd = cmd
       @out = out

spec/database_spec.rb

@@ -91,7 +91,9 @@ module SequenceServer
 
     it 'can tell FASTA files that are yet to be made into a BLAST+ database' do
       SequenceServer.config[:database_dir] = database_dir_unformatted
-      Database.scan_databases_dir
+      # rubocop:disable Style/RescueModifier
+      Database.scan_databases_dir rescue NO_BLAST_DATABASE_FOUND
+      # rubocop:enable Style/RescueModifier
       Database.unformatted_fastas.should_not be_empty
     end