sequenceserver 2.0.0.rc1 → 2.0.0.rc2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: a05949fcff69da464c286499cb974ea9c2cbe2c2
-  data.tar.gz: 5b697c08198c4424561fa226136719d2fb49c3cd
+SHA256:
+  metadata.gz: 164573dfee9002d6a1e164899e5d6f8a22696d7a13e3f6d48dd96a134673d8b3
+  data.tar.gz: 06fd8269f49b72a04d41d05903e7d7273e647d4e451047722d285840fecd207f
 SHA512:
-  metadata.gz: 9bdb8c9a31a2323d587c1f1e3a79357c22b0c4f6b0612e5872b1c0f6a6e1f7c720718ae7ef9e0f168dc0d420957cfa98d72ae6335c888c2360c609a8d98c21b8
-  data.tar.gz: d58521faa39150d36ac2df81b21ad68e80d8c465e792049ff10ca46e7ca8a60fb84a9f43404eb01c4efa8c799796e645108e0a46cb53b8494c30a9657a50a8b1
+  metadata.gz: a3d66c251f7f5e3a96a45878001245a49c811e02bebeac271a350ec9b8e944e8066cabf55c8851bf4e4ce1d6e9cd86e3b76cce53bde7f6230afd3db4592a9175
+  data.tar.gz: 14cdb61bbfbf1fb316df829aaf2c602c0753db51174b5166bb8c4de646ac43a2f5a0023593e063cd12c05e3dcf4163df1f48551e190df12607206afa0593ae5a

data/bin/sequenceserver

@@ -20,6 +20,30 @@ def download_from_url(url)
   system(cmd)
 end
 
+def ask_to_join
+  asked_to_join = File.join(SequenceServer::DOTDIR, 'asked_to_join')
+  unless File.exist?(asked_to_join)
+    puts
+    puts <<~MSG
+    Do you want to be notified of SequenceServer releases and any
+    other important announcements (3-12 messages a year)? If yes,
+    please provide your email address below or press enter to
+    continue (you won't be prompted again).
+    MSG
+    print '>> '
+    response = STDIN.gets.to_s.strip
+    puts
+
+    if response =~ /@/
+      post_email_cmd = "curl -m 5 https://docs.google.com/forms/u/0/d/e/" \
+      "1FAIpQLSe7sOCiKzYbI7LwErid-g3wfIU5Zpi6VTm0ILJyR036RqC8zg/formResponse " \
+      "-d ifq -d emailAddress=#{response} -d submit=Submit > /dev/null 2> /dev/null"
+      system post_email_cmd
+    end
+    system "touch #{asked_to_join}"
+  end
+end
+
 begin
   Slop.parse!(strict: true, help: true) do
     banner <<~BANNER
@@ -379,6 +403,8 @@ begin
 
       SequenceServer.config.write_config_file if fetch_option(:set).value
 
+      ask_to_join
+
       SequenceServer.run
     end
   end
@@ -386,4 +412,4 @@ rescue Slop::Error => e
   puts e
   puts "Run '#{$PROGRAM_NAME} -h' for help with command line options."
   exit
-end
+end

data/lib/sequenceserver/blast/report.rb

@@ -41,7 +41,8 @@ module SequenceServer
           h
         }.update(search_id: job.id,
                  submitted_at: job.submitted_at.utc,
-                 imported_xml: !!job.imported_xml_file).to_json
+                 imported_xml: !!job.imported_xml_file,
+                 seqserv_version: SequenceServer::VERSION).to_json
       end
 
       private

data/lib/sequenceserver/config.rb

@@ -81,7 +81,7 @@ module SequenceServer
     # otherwise.
     def parse_config_file
       unless file? config_file
-        logger.info "Configuration file not found: #{config_file}"
+        logger.debug "Configuration file not found: #{config_file}"
         return {}
       end
       logger.info "Reading configuration file: #{config_file}."

data/lib/sequenceserver/database.rb

@@ -328,11 +328,8 @@ module SequenceServer
         db_name
       end
 
-      # Guess whether FASTA file contains protein or nucleotide sequences based
-      # on first 32768 characters.
-      #
-      # NOTE: 2^15 == 32786. Approximately 546 lines, assuming 60 characters on
-      # each line.
+      # Guess whether FASTA file contains protein or nucleotide sequences by
+      # sampling a few few characters of the file.
       def guess_sequence_type_in_fasta(file)
         sequences = sample_sequences(file)
         sequence_types = sequences.map { |seq| Sequence.guess_type(seq) }
@@ -340,14 +337,14 @@ module SequenceServer
         (sequence_types.length == 1) && sequence_types.first
       end
 
-      # Read first 32768 characters of the file. Split on fasta def line
-      # pattern and return.
+      # Read first 1,048,576 characters of the file, split the read text on
+      # fasta def line pattern and return.
       #
       # If the given file is FASTA, returns Array of as many different
       # sequences in the portion of the file read. Returns the portion
       # of the file read wrapped in an Array otherwise.
       def sample_sequences(file)
-        File.read(file, 32_768).split(/^>.+$/).delete_if(&:empty?)
+        File.read(file, 1_048_576).split(/^>.+$/).delete_if(&:empty?)
       end
     end
   end

data/lib/sequenceserver/version.rb

@@ -1,4 +1,4 @@
 # Define version number.
 module SequenceServer
-  VERSION = '2.0.0.rc1'.freeze
+  VERSION = '2.0.0.rc2'.freeze
 end

data/public/css/sequenceserver.css

@@ -33,6 +33,10 @@ label:hover {
   color: #c74f14;
 }
 
+.yellow-background {
+  background-color: #E2D382;
+}
+
 /**
  * Disable resize grabber on textarea.
  */