rbbt-marq 2.1.0 → 2.1.1

data/install_scripts/rake_includes.rb

@@ -47,14 +47,14 @@ task 'data' do
 
   Progress.monitor("Processing #{platforms.keys.length} platforms") if platforms.keys.length > 1
   platforms.each{|platform, datasets|
-
     begin
       # Prepare the platform
       MARQ::Platform.process(platform)
     rescue
       puts "Error processing platform #{platform}"
       puts $!.message
-      puts $!.backtrace.join("\n")
+      puts "\n" * 3
+      #puts $!.backtrace.join("\n")
       next
     end
     
@@ -63,7 +63,7 @@ task 'data' do
     $changes = false
     # Process all datasets
     
-    Progress.monitor("Processing #{datasets.length} datasets") if datasets.length > 1
+    Progress.monitor("Processing #{datasets.length} datasets", :announcement => Proc.new{|d| "Dataset #{ d }" }) if datasets.length > 1
     datasets.each{|dataset|
       begin
         already_processed = MARQ::Dataset.exists?(dataset) || MARQ::Dataset.broken?(dataset)
@@ -74,10 +74,11 @@ task 'data' do
       rescue
         puts "Error processing dataset #{ dataset }"
         puts $!.message
-        puts $!.backtrace.join("\n")
+        puts "\n" * 3
+        #puts $!.backtrace.join("\n")
       end
     }
-
+    
     # Mark the platform for saving in DB
     platforms_to_save << platform if $changes || $update_db
   }
@@ -89,7 +90,8 @@ task 'data' do
     rescue
       puts "Error saving platform #{ platform }"
       puts $!.message
-      puts $!.backtrace.join("\n")
+      puts "\n" * 3
+      #puts $!.backtrace.join("\n")
     end
   }
 end
@@ -97,7 +99,10 @@ end
 def annotations(name, cross_platform = false, &block)
   platforms = process_list
 
+  Progress.monitor("Processing #{platforms.keys.length} platforms for #{ name } annotations")
   platforms.each do |platform, datasets|
+    next if ! MARQ::Platform.exists? platform
+    Progress.monitor("Processing #{datasets.length} datasets", :announcement => Proc.new{|d| "Dataset #{ d }" }) if datasets.length > 1
     datasets.each do |dataset|
       begin
         next if File.exist?(File.join("annotations", name, dataset)) && ! $force
@@ -247,7 +252,7 @@ end
 task 'default' do
   Rake::Task['data'].invoke
   Rake::Task['annotate_Words'].invoke
-  Rake::Task['annotate_UMLS'].invoke
-  Rake::Task['annotate_Polysearch'].invoke
+  #Rake::Task['annotate_UMLS'].invoke
+  #Rake::Task['annotate_Polysearch'].invoke
   Rake::Task['annotate_GO'].invoke
 end

data/lib/MARQ/GEO.rb

@@ -10,6 +10,8 @@ module GEO
 
   DATA_DIR = File.join(MARQ.datadir, 'GEO')
 
+  PLATFORM_BLACKLIST = %w(GPL4065)
+
   # Get information from Entrez
   module Remote
 
@@ -178,10 +180,11 @@ module GEO
     end
 
     def self.GPL(platform)
-
       if !File.exist?(File.join(DATA_DIR, 'platforms',"#{platform}.yaml"))  &&
          !File.exist?(File.join(DATA_DIR, 'platforms',"#{platform}.skip")) 
         begin
+          raise "Platform Blacklisted" if PLATFORM_BLACKLIST.include? platform
+
           if platform =~ /_/
             organism =  GPL(platform.match(/(.*?)_/)[1])[:organism]
 
@@ -443,8 +446,8 @@ module GEO
     # Load GPL data. Translates IDS of the platform probes using AILUN and our
     # system (called biomart for clarity)
     def self.GPL(platform)
-      path = GEO::platform_path(platform)
-      return if path.nil? || File.exist?(path)
+      path = File.join(DATA_DIR, platform)
+      return if File.exist?(path)
 
       if platform =~ /_/
         FileUtils.mkdir(path)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-marq
 version: !ruby/object:Gem::Version 
-  version: 2.1.0
+  version: 2.1.1
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -9,7 +9,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-02-12 00:00:00 +01:00
+date: 2010-02-15 00:00:00 +01:00
 default_executable: marq_config
 dependencies: 
 - !ruby/object:Gem::Dependency