sequenceserver 1.1.0.beta3 → 1.1.0.beta4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2e60bdefc921484208426a507ff32229e5945b1b
-  data.tar.gz: 85a162161cae976cc790ae3fed7b06ab81f11786
+  metadata.gz: a526ad89575f0b9118bf986359b9750a2a1ef894
+  data.tar.gz: 3fa16082e5bb2b99c16be95413ba0fbdf722baf4
 SHA512:
-  metadata.gz: c4511c2651001127d25f0b319984ed4cbc5b4e4d6dccde42823b1c33fd14a99e86045d8416da1d8e514e6825df44933359d32eafe1167e0bdb30243d2017a295
-  data.tar.gz: 3917c29dfb8be319b92029295f3996338195aa3bab09a176c625b22e1f7b7fe56588aedf8d16b8724aa07acdfbe35c1c3982a3f2a3bbf47d165745d11cef4523
+  metadata.gz: 2b95e0a703717cd2af830462624dcea36c10b103cffaa3fb4f80e811abe54625a070d94caefe8c05f26fc59fa41ebaa06c80091b8a0b88b0286f8597d5cea2fd
+  data.tar.gz: 5a4e459777fe4ecf68e1f80c0aee8aadb8b231e2dd11bbee79b51ef16f1907c2b6ff69751552daa7bca3c927b38d5f92b9b9123ae537862a016e7b368011c8f2

data/lib/sequenceserver/api_errors.rb

@@ -18,6 +18,8 @@ module SequenceServer
     def message
       'The requested job could not be found'
     end
+
+    undef_method :backtrace
   end
 
   # Errors caused due to incorrect user input.

data/lib/sequenceserver/blast/formatter.rb

@@ -11,20 +11,20 @@ module SequenceServer
       extend Forwardable
       def_delegators SequenceServer, :config, :logger, :sys
 
-      def initialize(archive_file, type)
-        @archive_file = archive_file
+      def initialize(job, type)
+        @job = job
         @format, @mime, @specifiers = OUTFMT[type]
         @type = type
 
         validate && run
       end
 
-      attr_reader :archive_file, :type
+      attr_reader :job, :type
 
       attr_reader :format, :mime, :specifiers
 
       def file
-        @file ||= File.join(File.dirname(archive_file), filename)
+        @file ||= File.join(job.dir, filename)
       end
 
       def filename
@@ -37,7 +37,7 @@ module SequenceServer
       def run
         return if File.exist?(file)
         command =
-          "blast_formatter -archive '#{archive_file}'" \
+          "blast_formatter -archive '#{job.stdout}'" \
           " -outfmt '#{format} #{specifiers}'" \
           " -out '#{file}'"
         sys(command, path: config[:bin], dir: DOTDIR)
@@ -46,12 +46,9 @@ module SequenceServer
       end
 
       def validate
-        return true if archive_file && format &&
-                       File.exist?(archive_file)
-        fail InputError, <<MSG
-Incorrect request parameters. Please ensure that requested file name is
-correct and the file type is either xml or tsv.
-MSG
+        fail SystemError if !File.exist?(job.stdout) ||
+          File.zero?(job.stdout)
+        true
       end
     end
   end

data/lib/sequenceserver/blast/job.rb

@@ -33,8 +33,16 @@ module SequenceServer
 
       # BLAST's exit status is not definitive of success or error, so we
       # override success? to define custom criteria. :TODO:
-      def success?
-        super
+      def raise!
+        return true if exitstatus == 0
+
+        stderr = File.readlines(this.stderr)
+        if exitstatus == 1 # error in query sequence or options; see [1]
+          error = stderr.grep(ERROR_LINE)
+          error = stderr if error.empty?
+          fail InputError, error.join
+        end
+        fail SystemError, stderr.join
       end
 
       private

data/lib/sequenceserver/blast/report.rb

@@ -43,27 +43,15 @@ module SequenceServer
 
       # Generate report.
       def generate
-        assert_job_completed_successfully
-        xml_ir = parse_xml File.read(Formatter.run(job.stdout, 'xml').file)
-        tsv_ir = parse_tsv File.read(Formatter.run(job.stdout, 'custom_tsv').file)
+        job.raise!
+        xml_ir = parse_xml File.read(Formatter.run(job, 'xml').file)
+        tsv_ir = parse_tsv File.read(Formatter.run(job, 'custom_tsv').file)
         extract_program_info xml_ir
         extract_params xml_ir
         extract_stats xml_ir
         extract_queries xml_ir, tsv_ir
       end
 
-      def assert_job_completed_successfully
-        return true if job.success?
-
-        stderr = File.readlines(job.stderr)
-        if job.exitstatus == 1 # error in query sequence or options; see [1]
-          error = stderr.grep(ERROR_LINE)
-          error = stderr if error.empty?
-          fail InputError, error.join
-        end
-        fail SystemError, stderr.join
-      end
-
       # Make program name and program name + version available via `program`
       # and `program_version` attributes.
       def extract_program_info(ir)
@@ -107,10 +95,6 @@ module SequenceServer
         xml_ir[8].each do |n|
           query = Query.new(self, n[0], n[2], n[3], [])
           extract_hits(n[4], tsv_ir[query.id], query)
-          query.hits = query.hits.sort_by do |h|
-            first_hsp = h.hsps.first # most significant hsp
-            [first_hsp.evalue, first_hsp.score]
-          end
           queries << query
         end
       end
@@ -131,9 +115,6 @@ module SequenceServer
           hit = Hit.new(query, n[0], n[1], n[3], n[2], n[4],
                         tsv_ir[n[1]][0], tsv_ir[n[1]][1],[])
           extract_hsps(n[5], tsv_ir[n[1]][2], hit)
-          hit.hsps = hit.hsps.sort_by do |h|
-            [h.evalue, h.score]
-          end
           query.hits << hit
         end
       end

data/lib/sequenceserver/job.rb

@@ -63,6 +63,10 @@ module SequenceServer
       mkdir_p dir
       yield if block_given?
       save
+    rescue Errno::ENOSPC
+      raise SystemError
+    rescue Errno::EACCES
+      raise SystemError
     rescue => e
       rm_rf dir
       raise e
@@ -70,6 +74,12 @@ module SequenceServer
 
     attr_reader :id, :completed_at, :exitstatus
 
+    # Returns shell command that will be executed. Subclass needs to provide a
+    # concrete implementation.
+    def command
+      raise "Not implemented."
+    end
+
     # Shell out and execute the job.
     #
     # NOTE: This method is called asynchronously by thread pool.
@@ -80,10 +90,16 @@ module SequenceServer
       done! e.exitstatus
     end
 
-    # Returns shell command that will be executed. Subclass needs to provide a
-    # concrete implementation.
-    def command
-      raise "Not implemented."
+    # Is exitstatus of the job available? If yes, it means the job is done.
+    def done?
+      !!@exitstatus
+    end
+
+    # Raise RuntimeError if job finished with non-zero exit status. This method
+    # should be called on a completed job before attempting to use the results.
+    # Subclasses should provide their own implementation.
+    def raise!
+      raise if done? && exitstatus != 0
     end
 
     # Where will the stdout be written to during execution and read from later.
@@ -96,14 +112,9 @@ module SequenceServer
       File.join(dir, 'stderr')
     end
 
-    # Was the job successful?
-    def success?
-      exitstatus == 0
-    end
-
-    # Is the job done? Yes if exitstatus of the job is available. No otherwise.
-    def done?
-      !!@exitstatus
+    # Where to save all kind of data for this job.
+    def dir
+      File.join(DOTDIR, id)
     end
 
     private
@@ -144,11 +155,6 @@ module SequenceServer
       save
     end
 
-    # Where to save all kind of data for this job.
-    def dir
-      File.join(DOTDIR, id)
-    end
-
     # Where to write serialised job object.
     def yfile
       File.join(dir, 'job.yaml')

data/lib/sequenceserver/job_remover.rb

@@ -8,7 +8,7 @@ module SequenceServer
   # be deleted as soon as they are done, or it can be Infinity in which case
   # jobs will never be deleted. Default is to delete finished jobs after 7 days.
   class JobRemover
-    DEFAULT_JOB_LIFETIME = 10080 # minutes (24 hrs = 7 days)
+    DEFAULT_JOB_LIFETIME = 43200 # minutes (i.e., 30 days)
 
     def initialize(job_lifetime)
       @job_lifetime = job_lifetime || DEFAULT_JOB_LIFETIME

data/lib/sequenceserver/routes.rb

@@ -122,19 +122,38 @@ module SequenceServer
     # Download BLAST report in various formats.
     get '/download/:jid.:type' do |jid, type|
       job = Job.fetch(jid)
-      out = BLAST::Formatter.new(job.rfile, type)
+      out = BLAST::Formatter.new(job, type)
       send_file out.file, :filename => out.filename, :type => out.mime
     end
 
-    # Catches any exception raised within the app and returns error message and
-    # the backtrace as response body. If the error class defines `http_status`
-    # instance method, its return value will be used to set HTTP status. HTTP
-    # status is set to 500 otherwise.
+    # Catches any exception raised within the app and returns JSON
+    # representation of the error:
+    # {
+    #    title: ...,     // plain text
+    #    message: ...,   // plain or HTML text
+    #    more_info: ..., // pre-formatted text
+    # }
+    #
+    # If the error class defines `http_status` instance method, its return
+    # value will be used to set HTTP status. HTTP status is set to 500
+    # otherwise.
+    #
+    # If the error class defines `title` instance method, its return value
+    # will be used as title. Otherwise name of the error class is used as
+    # title.
+    #
+    # If the error class defines `more_info` instance method, its return
+    # value will be used as more_info, otherwise `backtrace.join("\n")`
+    # is used as more_info. If an error class does not want to include
+    # more_info (like for NotFound), the error class must undefine
+    # `backtrace` method.
+    #
+    # All error classes should define `message` instance method.
     error 400..500 do
       error = env['sinatra.error']
 
       # All errors will have a message.
-      error_data = {message: error.message}
+      error_data = { message: error.message }
 
       # If error object has a title method, use that, or use error class for
       # title.
@@ -149,7 +168,7 @@ module SequenceServer
       # more_info.
       if error.respond_to? :more_info
         error_data[:more_info] = error.more_info
-      else
+      elsif error.respond_to? :backtrace
         error_data[:more_info] = error.backtrace.join("\n")
       end
 

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '1.1.0.beta3'
+  VERSION = '1.1.0.beta4'
 end

data/public/css/sequenceserver.css

@@ -28,7 +28,8 @@ a:hover, .btn-link:hover {
  * Disable resize grabber on textarea.
  */
 textarea {
-  resize: none;
+  resize: vertical;
+  min-height: 214px;
 }
 
 /**