workflow_manager 0.7.8 → 0.7.9

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: bb29ff98b1a798d31a2a6d3bc84b0a2145d975e8b5e30ef242f309eb74edd099
+  data.tar.gz: 8214d4df1d712c8926e771999105201f141c2495a86008c0dd661b45f6826ad3
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data/lib/job_checker.rb

@@ -43,15 +43,15 @@ class JobChecker
     end
     new_job_script
   end
-  def update_time_status(status, script_basename, user, project_number, next_dataset_id, rails_host)
+  def update_time_status(status, script_basename, user, project_number, next_dataset_id, rails_host, log_dir)
     unless @start_time
       @start_time = Time.now.strftime("%Y-%m-%d %H:%M:%S")
     end
     time = Time.now.strftime("%Y-%m-%d %H:%M:%S")
-    [status, script_basename, [@start_time, time].join("/"), user, project_number, next_dataset_id, rails_host].join(',')
+    [status, script_basename, [@start_time, time].join("/"), user, project_number, next_dataset_id, rails_host, log_dir].join(',')
   end
 
-  def perform(job_id, script_basename, log_file, user, project_id, next_dataset_id=nil, rails_host=nil)
+  def perform(job_id, script_basename, log_file, user, project_id, next_dataset_id=nil, rails_host=nil, log_dir=nil, copy_command_template=nil)
     puts "JobID (in JobChecker): #{job_id}"
     db0 = Redis.new(port: PORT, db: 0) # state + alpha DB
     db1 = Redis.new(port: PORT, db: 1) # log DB
@@ -66,10 +66,10 @@ class JobChecker
       #print ret
       state = ret.split(/\n/).last.strip
       #puts "state: #{state}"
-      db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id, rails_host)
+      db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id, rails_host, log_dir)
 
       unless state == pre_state
-        db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id, rails_host)
+        db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id, rails_host, log_dir)
         project_jobs = eval((db2[project_id]||[]).to_s)
         project_jobs = Hash[*project_jobs]
         project_jobs[job_id] = state
@@ -79,10 +79,22 @@ class JobChecker
       pre_state = state
       sleep WORKER_INTERVAL
     end while state =~ /RUNNING/  or state =~ /PENDING/ or state =~ /---/
+
+    # post process
     if next_dataset_id and rails_host
       uri = URI("#{rails_host}/data_set/#{next_dataset_id}/update_completed_samples")
       #p uri
       res = Net::HTTP.get_response(uri)
+
+      if log_dir and !log_dir.empty?
+        copy_command = copy_command_template.gsub("org_file", log_file)
+        #puts "copy_command=#{copy_command}"
+        system copy_command
+        err_file = log_file.gsub('_o.log','_e.log')
+        copy_command = copy_command_template.gsub("org_file", err_file)
+        #puts "copy_command=#{copy_command}"
+        system copy_command
+      end
     end
   end
 end

data/lib/workflow_manager/server.rb

@@ -187,12 +187,13 @@ module WorkflowManager
         statuses.each do |job_id, status|
           # puts [job_id, status].join(",")
           # 120249,RUNNING,QC_ventricles_100k.sh,2021-07-30 09:47:04/2021-07-30 09:47:04,masaomi,1535
-          stat, script_basename, time, user, project_number, next_dataset_id, rails_host = status.split(",")
+          stat, script_basename, time, user, project_number, next_dataset_id, rails_host, log_dir = status.split(",")
           if stat == "RUNNING" or stat == "PENDING"
             log_file = logs[job_id]
             log_puts("JobID (in recovery check): #{job_id}")
             puts "JobID (in recovery check): #{job_id}"
-            JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id, rails_host)
+            copy_command_template = copy_commands("org_file", log_dir).first
+            job_checker = JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id, rails_host, log_dir, copy_command_template)
           end
         end
       end
@@ -304,8 +305,10 @@ module WorkflowManager
       #p log_file
       #p job_id
       puts "JobID (in WorkflowManager): #{job_id}"
+      #puts "log_dir=#{log_dir}"
       sleep 1
-      JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id, rails_host)
+      copy_command_template = copy_commands("org_file", log_dir).first
+      job_checker = JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id, rails_host, log_dir, copy_command_template)
       job_id
     end
     def start_monitoring2(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='')

data/lib/workflow_manager/version.rb

@@ -1,3 +1,3 @@
 module WorkflowManager
-  VERSION = "0.7.8"
+  VERSION = "0.7.9"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: workflow_manager
 version: !ruby/object:Gem::Version
-  version: 0.7.8
+  version: 0.7.9
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-11-04 00:00:00.000000000 Z
+date: 2021-12-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler