workflow_manager 0.1.2 → 0.1.7

data/lib/workflow_manager/cluster.rb

@@ -26,7 +26,7 @@ module WorkflowManager
     end
     def job_ends?(log_file)
     end
-    def copy_commands(org_dir, dest_parent_dir)
+    def copy_commands(org_dir, dest_parent_dir, now=nil)
     end
     def kill_command(job_id)
     end
@@ -67,7 +67,7 @@ module WorkflowManager
       result = `#{command}`
       result.to_s.empty? ? false : true
     end
-    def copy_commands(org_dir, dest_parent_dir)
+    def copy_commands(org_dir, dest_parent_dir, now=nil)
       commands = []
       commands << "mkdir -p #{dest_parent_dir}"
       commands << "cp -r #{org_dir} #{dest_parent_dir}"
@@ -108,7 +108,7 @@ module WorkflowManager
     end
     def job_ends?(log_file)
       log_flag = false
-      IO.popen("tail -n 10 #{log_file}") do |io|
+      IO.popen("tail -n 10 #{log_file} 2> /dev/null") do |io|
         while line=io.gets
           if line =~ /__SCRIPT END__/
             log_flag = true
@@ -118,8 +118,12 @@ module WorkflowManager
       end
       log_flag
     end
-    def copy_commands(org_dir, dest_parent_dir)
-      commands = ["g-req -w copy #{org_dir} #{dest_parent_dir}"]
+    def copy_commands(org_dir, dest_parent_dir, now=nil)
+      commands = if now
+                   ["g-req copynow #{org_dir} #{dest_parent_dir}"]
+                 else
+                   ["g-req -w copy #{org_dir} #{dest_parent_dir}"]
+                 end
     end
     def kill_command(job_id)
       command = "qdel #{job_id}"
@@ -130,7 +134,7 @@ module WorkflowManager
   end
 
   class FGCZCourseCluster < FGCZCluster
-    def copy_commands(org_dir, dest_parent_dir)
+    def copy_commands(org_dir, dest_parent_dir, now=nil)
       commands = ["cp -r #{org_dir} #{dest_parent_dir}"]
     end
     def delete_command(target)

data/lib/workflow_manager/server.rb

@@ -107,8 +107,8 @@ module WorkflowManager
     def hello
       'hello, '+ @cluster.name
     end
-    def copy_commands(org_dir, dest_parent_dir)
-      @cluster.copy_commands(org_dir, dest_parent_dir)
+    def copy_commands(org_dir, dest_parent_dir, now=nil)
+      @cluster.copy_commands(org_dir, dest_parent_dir, now)
     end
     def kill_job(job_id)
       status(job_id, 'fail')
@@ -251,7 +251,7 @@ module WorkflowManager
         end
       #@statuses.close
       end
-      s.sort.reverse.map{|v| v.join(',')}.join("\n")
+      s.sort_by{|key, value| value.split(',')[2]}.reverse.map{|v| v.join(',')}.join("\n")
     end
     def get_log(job_id, with_err=false)
       log_file = nil

data/lib/workflow_manager/version.rb

@@ -1,3 +1,3 @@
 module WorkflowManager
-  VERSION = "0.1.2"
+  VERSION = "0.1.7"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: workflow_manager
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.7
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-30 00:00:00.000000000 Z
+date: 2014-12-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler