workflow_manager 0.7.6 → 0.7.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 2ae4ffec963b02a83f37a3034af4af3835e9b27e018d05b7294979e716b3ec47
+  metadata.gz: aff589c219150c4a2b7e8676d8540343143a12099ce4bfed847663e37f946a99
+  data.tar.gz: 64461e67991613603227c3894aa2b728db4952739071d140c007caefd8564601
 SHA512:
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-  data.tar.gz: 2c82352987cfcbfced6fe32bbe6a38544788b4d686277bd785a67a719ad22fef052102623388aec7bece99c059b7eb9c921bd07de695097cde7a87177f2ad26e
+  metadata.gz: 4e79f54d8335b4df34e466055d76cb8f64fa5c53787bf83047a7e259e5d564b0514e39d2b08ba56830dc73e9235164904806a34210e76e6e1018516e1f3bd243
+  data.tar.gz: 9e3f4b1ce2adddc6b4b13e77e7bedbef74c9b635253ba77f9dbd0d731a5a6896a515404b481aa0c7f23b1a739f55142f5825fa7b7ffa8ecb8f7c7a3ba8754166

data/config/environments/redis.conf

@@ -6,4 +6,4 @@ rdbcompression yes
 dir ./dbs
 dbfilename redis.rdb
 maxmemory 10gb
-port 6380
+port 6379

data/lib/job_checker.rb

@@ -1,6 +1,9 @@
 require 'sidekiq'
 require 'redis'
 
+require 'uri'
+require 'net/http'
+
 WORKER_INTERVAL = 10 # [s]
 REDIS_CONF = File.expand_path("../../config/environments/redis.conf", __FILE__)
 PORT = if File.exist?(REDIS_CONF)
@@ -40,15 +43,15 @@ class JobChecker
     end
     new_job_script
   end
-  def update_time_status(status, script_basename, user, project_number, next_dataset_id)
+  def update_time_status(status, script_basename, user, project_number, next_dataset_id, rails_host)
     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].join(',')
+    [status, script_basename, [@start_time, time].join("/"), user, project_number, next_dataset_id, rails_host].join(',')
   end
 
-  def perform(job_id, script_basename, log_file, user, project_id, next_dataset_id=nil)
+  def perform(job_id, script_basename, log_file, user, project_id, next_dataset_id=nil, rails_host=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
@@ -63,10 +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)
+      db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id, rails_host)
 
       unless state == pre_state
-        db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id)
+        db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id, rails_host)
         project_jobs = eval((db2[project_id]||[]).to_s)
         project_jobs = Hash[*project_jobs]
         project_jobs[job_id] = state
@@ -76,6 +79,11 @@ class JobChecker
       pre_state = state
       sleep WORKER_INTERVAL
     end while state =~ /RUNNING/  or state =~ /PENDING/ or state =~ /---/
+    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)
+    end
   end
 end
 

data/lib/workflow_manager/server.rb

@@ -187,12 +187,12 @@ 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 = status.split(",")
+          stat, script_basename, time, user, project_number, next_dataset_id, rails_host = 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)
+            JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id, rails_host)
           end
         end
       end
@@ -297,7 +297,7 @@ module WorkflowManager
         Thread.current.kill
       end
     end
-    def start_monitoring3(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='', next_dataset_id='')
+    def start_monitoring3(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='', next_dataset_id='', rails_host=nil)
       script_basename = File.basename(script_path)
       job_id, log_file, command = @cluster.submit_job(script_path, script_content, sge_options)
       #p command
@@ -305,7 +305,7 @@ module WorkflowManager
       #p job_id
       puts "JobID (in WorkflowManager): #{job_id}"
       sleep 1
-      JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id)
+      JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id, rails_host)
       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 = "0.7.6"
+  VERSION = "0.7.7"
 end

data/start_workflow_manager.sh

@@ -8,4 +8,4 @@ which g-sub
 which g-req
 mkdir -p logs
 mkdir -p dbs
-bundle exec workflow_manager -d druby://fgcz-h-031:40001
+bundle exec workflow_manager -d druby://fgcz-h-032:40002

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: workflow_manager
 version: !ruby/object:Gem::Version
-  version: 0.7.6
+  version: 0.7.7
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-10-01 00:00:00.000000000 Z
+date: 2021-10-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler