sequenceserver 2.0.0.rc8 → 2.1.0

data/lib/sequenceserver/zip_file_generator.rb

@@ -0,0 +1,56 @@
+# Source: https://github.com/rubyzip/rubyzip/blob/9d891f7353e66052283562d3e252fe380bb4b199/samples/example_recursive.rb
+
+require 'zip'
+
+# This is a simple example which uses rubyzip to
+# recursively generate a zip file from the contents of
+# a specified directory. The directory itself is not
+# included in the archive, rather just its contents.
+#
+# Usage:
+#   directory_to_zip = "/tmp/input"
+#   output_file = "/tmp/out.zip"
+#   zf = ZipFileGenerator.new(directory_to_zip, output_file)
+#   zf.write()
+class ZipFileGenerator
+  # Initialize with the directory to zip and the location of the output archive.
+  def initialize(input_dir, output_file)
+    @input_dir = input_dir
+    @output_file = output_file
+  end
+
+  # Zip the input directory.
+  def write
+    entries = Dir.entries(@input_dir) - %w[. ..]
+
+    ::Zip::File.open(@output_file, ::Zip::File::CREATE) do |zipfile|
+      write_entries entries, '', zipfile
+    end
+  end
+
+  private
+
+  # A helper method to make the recursion work.
+  def write_entries(entries, path, zipfile)
+    entries.each do |e|
+      zipfile_path = path == '' ? e : File.join(path, e)
+      disk_file_path = File.join(@input_dir, zipfile_path)
+
+      if File.directory? disk_file_path
+        recursively_deflate_directory(disk_file_path, zipfile, zipfile_path)
+      else
+        put_into_archive(disk_file_path, zipfile, zipfile_path)
+      end
+    end
+  end
+
+  def recursively_deflate_directory(disk_file_path, zipfile, zipfile_path)
+    zipfile.mkdir zipfile_path
+    subdir = Dir.entries(disk_file_path) - %w[. ..]
+    write_entries subdir, zipfile_path, zipfile
+  end
+
+  def put_into_archive(disk_file_path, zipfile, zipfile_path)
+    zipfile.add(zipfile_path, disk_file_path)
+  end
+end

data/lib/sequenceserver.rb

@@ -5,11 +5,7 @@ require 'resolv'
 # Top level module / namespace.
 module SequenceServer
   # The default version of BLAST that will be downloaded and configured for use.
-  BLAST_VERSION = '2.10.0+'.freeze
-  # The minimum version of BLAST that SequenceServer is happy to run with. This
-  # is for compatiblity with older database formats. Users will download BLAST
-  # themselves.
-  MIN_BLAST_VERSION = '2.9.0+'.freeze
+  BLAST_VERSION = '2.12.0+'.freeze
 
   # Default location of configuration file.
   DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'.freeze
@@ -28,6 +24,7 @@ module SequenceServer
   require 'sequenceserver/job_remover'
   require 'sequenceserver/exceptions'
   require 'sequenceserver/sys'
+  require 'sequenceserver/refinements'
 
   # The singleton methods defined below constitute the "runtime" environment of
   # SequenceServer.
@@ -78,9 +75,9 @@ module SequenceServer
       Thread.abort_on_exception = true if development?
 
       # Now locate binaries, scan databases directory, require any plugin files.
+      load_extension
       init_binaries
       init_database
-      load_extension
 
       # The above methods validate bin dir, database dir, and path to plugin
       # files. Port and host settings don't need to be validated: if running
@@ -141,7 +138,8 @@ module SequenceServer
         puts "     -  http://#{ip_address}:#{config[:port]}"
         puts "     -  http://#{hostname}:#{config[:port]}" if hostname
         puts '   To share your setup with anyone in the world, ask your IT team'
-        puts '   for a public IP address.'
+        puts '   for a public IP address or consider the SequenceServer cloud'
+        puts '   hosting service: https://sequenceserver.com/cloud'
         puts '   To disable sharing, set :host: key in config file to 127.0.0.1'
         puts '   and restart server.'
       end
@@ -205,12 +203,19 @@ module SequenceServer
 
       makeblastdb.scan
       fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if !makeblastdb.any_formatted?
-      fail INCOMPATIBLE_BLAST_DATABASES, config[:database_dir] if makeblastdb.any_incompatible?
 
       Database.collection = makeblastdb.formatted_fastas
       Database.each do |database|
-        logger.debug("Found #{database.type} database '#{database.title}'" \
-                     " at '#{database.name}'")
+        logger.debug "Found #{database.type} database '#{database.title}' at '#{database.path}'"
+        if database.non_parse_seqids?
+          logger.warn "Database '#{database.title}' was created without using the" \
+                      ' -parse_seqids option of makeblastdb. FASTA download will' \
+                      " not work correctly (path: '#{database.path}')."
+        elsif database.v4?
+          logger.warn "Database '#{database.title}' is of older format. Mixing" \
+                      ' old and new format databases can be problematic' \
+                      "(path: '#{database.path}')."
+        end
       end
     end
 
@@ -245,7 +250,7 @@ module SequenceServer
       end
       version = out.split[1]
       fail BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE if version.empty?
-      fail BLAST_NOT_COMPATIBLE, version unless is_compatible(version, MIN_BLAST_VERSION)
+      fail BLAST_NOT_COMPATIBLE, version unless is_compatible(version, BLAST_VERSION)
     end
 
     def server_url

data/public/config.js

@@ -25,14 +25,19 @@ System.config({
     "jquery": "github:components/jquery@2.1.4",
     "jquery-ui": "github:components/jqueryui@1.11.4",
     "nicgirault/circosJs": "github:nicgirault/circosJs@1.7.0",
-    "react": "npm:react@0.13.3",
+    "react": "npm:react@18.0.0",
+    "react-dom": "npm:react-dom@18.0.0",
     "underscore": "npm:underscore@1.8.3",
+    "vakata/jstree": "github:vakata/jstree@3.3.8",
     "webshim": "npm:webshim@1.15.8",
     "github:components/jqueryui@1.11.4": {
       "jquery": "github:components/jquery@2.1.4"
     },
-    "github:jspm/nodelibs-buffer@0.1.0": {
-      "buffer": "npm:buffer@3.4.3"
+    "github:jspm/nodelibs-assert@0.1.0": {
+      "assert": "npm:assert@1.5.0"
+    },
+    "github:jspm/nodelibs-buffer@0.1.1": {
+      "buffer": "npm:buffer@5.7.1"
     },
     "github:jspm/nodelibs-events@0.1.1": {
       "events": "npm:events@1.0.2"
@@ -40,8 +45,8 @@ System.config({
     "github:jspm/nodelibs-path@0.1.0": {
       "path-browserify": "npm:path-browserify@0.0.0"
     },
-    "github:jspm/nodelibs-process@0.1.1": {
-      "process": "npm:process@0.10.1"
+    "github:jspm/nodelibs-process@0.1.2": {
+      "process": "npm:process@0.11.10"
     },
     "github:jspm/nodelibs-stream@0.1.0": {
       "stream-browserify": "npm:stream-browserify@1.0.0"
@@ -49,39 +54,33 @@ System.config({
     "github:jspm/nodelibs-util@0.1.0": {
       "util": "npm:util@0.10.3"
     },
+    "github:jspm/nodelibs-vm@0.1.0": {
+      "vm-browserify": "npm:vm-browserify@0.0.4"
+    },
     "github:twbs/bootstrap@3.3.5": {
       "jquery": "github:components/jquery@2.1.4"
     },
-    "npm:amdefine@1.0.0": {
-      "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "module": "github:jspm/nodelibs-module@0.1.0",
-      "path": "github:jspm/nodelibs-path@0.1.0",
-      "process": "github:jspm/nodelibs-process@0.1.1"
+    "npm:assert@1.5.0": {
+      "assert": "github:jspm/nodelibs-assert@0.1.0",
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
+      "object-assign": "npm:object-assign@4.1.1",
+      "process": "github:jspm/nodelibs-process@0.1.2",
+      "util": "npm:util@0.10.3"
     },
     "npm:babel-runtime@5.8.20": {
-      "process": "github:jspm/nodelibs-process@0.1.1"
+      "process": "github:jspm/nodelibs-process@0.1.2"
     },
-    "npm:buffer@3.4.3": {
-      "base64-js": "npm:base64-js@0.0.8",
-      "ieee754": "npm:ieee754@1.1.6",
-      "is-array": "npm:is-array@1.0.1"
+    "npm:buffer@5.7.1": {
+      "base64-js": "npm:base64-js@1.5.1",
+      "ieee754": "npm:ieee754@1.2.1"
     },
     "npm:core-js@1.1.2": {
       "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "process": "github:jspm/nodelibs-process@0.1.1",
+      "process": "github:jspm/nodelibs-process@0.1.2",
       "systemjs-json": "github:systemjs/plugin-json@0.1.0"
     },
-    "npm:core-util-is@1.0.1": {
-      "buffer": "github:jspm/nodelibs-buffer@0.1.0"
-    },
-    "npm:envify@3.4.0": {
-      "jstransform": "npm:jstransform@10.1.0",
-      "process": "github:jspm/nodelibs-process@0.1.1",
-      "through": "npm:through@2.3.8"
-    },
-    "npm:esprima-fb@13001.1001.0-dev-harmony-fb": {
-      "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "process": "github:jspm/nodelibs-process@0.1.1"
+    "npm:core-util-is@1.0.3": {
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1"
     },
     "npm:font-awesome@4.4.0": {
       "css": "github:systemjs/plugin-css@0.1.15"
@@ -89,58 +88,66 @@ System.config({
     "npm:inherits@2.0.1": {
       "util": "github:jspm/nodelibs-util@0.1.0"
     },
-    "npm:jstransform@10.1.0": {
-      "base62": "npm:base62@0.1.1",
-      "buffer": "github:jspm/nodelibs-buffer@0.1.0",
-      "esprima-fb": "npm:esprima-fb@13001.1001.0-dev-harmony-fb",
+    "npm:loose-envify@1.4.0": {
       "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "process": "github:jspm/nodelibs-process@0.1.1",
-      "source-map": "npm:source-map@0.1.31"
+      "js-tokens": "npm:js-tokens@4.0.0",
+      "process": "github:jspm/nodelibs-process@0.1.2",
+      "stream": "github:jspm/nodelibs-stream@0.1.0",
+      "util": "github:jspm/nodelibs-util@0.1.0"
     },
     "npm:path-browserify@0.0.0": {
-      "process": "github:jspm/nodelibs-process@0.1.1"
+      "process": "github:jspm/nodelibs-process@0.1.2"
     },
-    "npm:react@0.13.3": {
-      "buffer": "github:jspm/nodelibs-buffer@0.1.0",
-      "envify": "npm:envify@3.4.0",
-      "process": "github:jspm/nodelibs-process@0.1.1"
+    "npm:process@0.11.10": {
+      "assert": "github:jspm/nodelibs-assert@0.1.0",
+      "fs": "github:jspm/nodelibs-fs@0.1.2",
+      "vm": "github:jspm/nodelibs-vm@0.1.0"
+    },
+    "npm:react-dom@18.0.0": {
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
+      "loose-envify": "npm:loose-envify@1.4.0",
+      "process": "github:jspm/nodelibs-process@0.1.2",
+      "react": "npm:react@18.0.0",
+      "scheduler": "npm:scheduler@0.21.0",
+      "stream": "github:jspm/nodelibs-stream@0.1.0"
     },
-    "npm:readable-stream@1.1.13": {
-      "buffer": "github:jspm/nodelibs-buffer@0.1.0",
-      "core-util-is": "npm:core-util-is@1.0.1",
+    "npm:react@18.0.0": {
+      "loose-envify": "npm:loose-envify@1.4.0",
+      "process": "github:jspm/nodelibs-process@0.1.2"
+    },
+    "npm:readable-stream@1.1.14": {
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1",
+      "core-util-is": "npm:core-util-is@1.0.3",
       "events": "github:jspm/nodelibs-events@0.1.1",
       "inherits": "npm:inherits@2.0.1",
       "isarray": "npm:isarray@0.0.1",
-      "process": "github:jspm/nodelibs-process@0.1.1",
+      "process": "github:jspm/nodelibs-process@0.1.2",
       "stream-browserify": "npm:stream-browserify@1.0.0",
       "string_decoder": "npm:string_decoder@0.10.31"
     },
-    "npm:source-map@0.1.31": {
-      "amdefine": "npm:amdefine@1.0.0",
-      "fs": "github:jspm/nodelibs-fs@0.1.2",
-      "path": "github:jspm/nodelibs-path@0.1.0",
-      "process": "github:jspm/nodelibs-process@0.1.1"
+    "npm:scheduler@0.21.0": {
+      "loose-envify": "npm:loose-envify@1.4.0",
+      "process": "github:jspm/nodelibs-process@0.1.2"
     },
     "npm:stream-browserify@1.0.0": {
       "events": "github:jspm/nodelibs-events@0.1.1",
       "inherits": "npm:inherits@2.0.1",
-      "readable-stream": "npm:readable-stream@1.1.13"
+      "readable-stream": "npm:readable-stream@1.1.14"
     },
     "npm:string_decoder@0.10.31": {
-      "buffer": "github:jspm/nodelibs-buffer@0.1.0"
-    },
-    "npm:through@2.3.8": {
-      "process": "github:jspm/nodelibs-process@0.1.1",
-      "stream": "github:jspm/nodelibs-stream@0.1.0"
+      "buffer": "github:jspm/nodelibs-buffer@0.1.1"
     },
     "npm:util@0.10.3": {
       "inherits": "npm:inherits@2.0.1",
-      "process": "github:jspm/nodelibs-process@0.1.1"
+      "process": "github:jspm/nodelibs-process@0.1.2"
+    },
+    "npm:vm-browserify@0.0.4": {
+      "indexof": "npm:indexof@0.0.1"
     },
     "npm:webshim@1.15.8": {
       "fs": "github:jspm/nodelibs-fs@0.1.2",
       "path": "github:jspm/nodelibs-path@0.1.0",
-      "process": "github:jspm/nodelibs-process@0.1.1"
+      "process": "github:jspm/nodelibs-process@0.1.2"
     }
   }
 });

data/public/css/fonts.css

@@ -3,28 +3,29 @@
  * http://stackoverflow.com/questions/11002820/why-should-we-include-ttf-eot-woff-svg-in-a-font-face
  * */
 @font-face {
-	font-family: 'Source Sans Pro';
-	font-style: normal;
-	font-weight: 400;
-	src:
-		local('Source Sans Pro'),
-		local('SourceSansPro-Regular'),
-		url('../fonts/Source_Sans_Pro_400.woff2') format('woff2'),
-		url('../fonts/Source_Sans_Pro_400.woff') format('woff'),
-		url('../fonts/Source_Sans_Pro_400.ttf') format('truetype'),
-		url('../fonts/Source_Sans_Pro_400.svg') format('svg'),
-		url('../fonts/Source_Sans_Pro_400.eot') format('embedded-opentype');
+  font-family: 'Source Sans Pro';
+  font-style: normal;
+  font-weight: 400;
+  src:
+    local('Source Sans Pro'),
+    local('SourceSansPro-Regular'),
+    url('../fonts/Source_Sans_Pro_400.woff2') format('woff2'),
+    url('../fonts/Source_Sans_Pro_400.woff') format('woff'),
+    url('../fonts/Source_Sans_Pro_400.ttf') format('truetype'),
+    url('../fonts/Source_Sans_Pro_400.svg') format('svg'),
+    url('../fonts/Source_Sans_Pro_400.eot') format('embedded-opentype');
 }
+
 @font-face {
-	font-family: 'Source Sans Pro';
-	font-style: normal;
-	font-weight: 700;
-	src:
-		local('Source Sans Pro Bold'),
-		local('SourceSansPro-Bold'),
-		url('../fonts/Source_Sans_Pro_700.woff2') format('woff2'),
-		url('../fonts/Source_Sans_Pro_700.woff') format('woff'),
-		url('../fonts/Source_Sans_Pro_700.ttf') format('truetype'),
-		url('../fonts/Source_Sans_Pro_700.svg') format('svg'),
-		url('../fonts/Source_Sans_Pro_700.eot') format('embedded-opentype');
+  font-family: 'Source Sans Pro';
+  font-style: normal;
+  font-weight: 700;
+  src:
+    local('Source Sans Pro Bold'),
+    local('SourceSansPro-Bold'),
+    url('../fonts/Source_Sans_Pro_700.woff2') format('woff2'),
+    url('../fonts/Source_Sans_Pro_700.woff') format('woff'),
+    url('../fonts/Source_Sans_Pro_700.ttf') format('truetype'),
+    url('../fonts/Source_Sans_Pro_700.svg') format('svg'),
+    url('../fonts/Source_Sans_Pro_700.eot') format('embedded-opentype');
 }