rbbt-util 5.5.11 → 5.5.12

checksums.yaml

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data/lib/rbbt/resource.rb

@@ -3,20 +3,21 @@ require 'rbbt/util/log'
 require 'rbbt/resource/path'
  
 module Resource
-  def self.extended(base)
-    if not base.respond_to? :pkgdir
-      class << base
-        attr_accessor :pkgdir, :subdir, :resources, :rake_dirs
-      end
+  def self.remote_servers
+    @remote_servers = Rbbt.etc.file_servers.exists? ? Rbbt.etc.file_servers.yaml : {}
+  end
 
-      base.pkgdir = 'rbbt'
-      base.subdir = ''
-      base.resources = {}
-      base.rake_dirs = {}
-    end
+  def self.extended(base)
+    base.pkgdir = 'rbbt'
+    base.subdir = ''
+    base.resources = {}
+    base.rake_dirs = {}
+    base.remote_server = Resource.remote_servers[base.to_s]
     base
   end
 
+  attr_accessor :pkgdir, :subdir, :resources, :rake_dirs, :remote_server
+
   def root()
     Path.setup @subdir || "", @pkgdir, self
   end
@@ -52,6 +53,20 @@ module Resource
     end
   end
 
+  def get_from_server(path, final_path)
+    url = File.join(remote_server, '/resource/', self.to_s, 'get_file')
+    url << "?" << Misc.hash2GET_params(:file => path, :create => false)
+    begin
+      Open.write(final_path, Open.read(url, :nocache => true))
+      return true
+    rescue
+      Log.warn "Could not retrieve (#{self.to_s}) #{ path } from #{ remote_server }"
+      Log.error $!.message
+      FileUtils.rm final_path if File.exists? final_path
+      return false
+    end
+  end
+
   def produce(path, force = false)
     case
     when @resources.include?(path)
@@ -68,6 +83,7 @@ module Resource
     if not File.exists? final_path or force
       Log.medium "Producing: #{ final_path }"
       Misc.lock final_path + '.produce' do
+        (remote_server and get_from_server(path, final_path)) or
         begin
           case type
           when :string

data/lib/rbbt/util/misc.rb

@@ -1,6 +1,7 @@
 require 'lockfile'
 require 'net/smtp'
 require 'digest/md5'
+require 'cgi'
 
 class Hash
   def chunked_values_at(keys, max = 5000)

data/test/rbbt/test_resource.rb

@@ -60,8 +60,16 @@ class TestTSV < Test::Unit::TestCase
   end
 
   def test_libdir
-    assert File.exists? TestResource[].share.lib.R["util.R"].find :lib
-    assert File.exists? TestResource[].share.lib.R["util.R"].find 
+    assert File.exists? TestResource[].share.Rlib["util.R"].find :lib
+    assert File.exists? TestResource[].share.Rlib["util.R"].find 
+  end
+
+  def __test_server
+    require 'rbbt/sources/organism'
+    TmpFile.with_file do |tmp|
+      Organism.get_from_server("Hsa/jun2011/identifiers", tmp)
+      assert Open.read(tmp).length > 10000
+    end
   end
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.5.11
+  version: 5.5.12
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-31 00:00:00.000000000 Z
+date: 2013-11-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake