workflow_manager 0.7.2 → 0.7.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 0e552d468cfdfad569630ee0f6db07c943935c74ff48fadef437f03cb3c3e8cd
-  data.tar.gz: 2642f5814e314301993a92e905e271bbc3d0b9a2ba9cfae37a0cd4d7026380e7
+  metadata.gz: e2da7b0c22f10f971c6dc3eb21c89b8321a8f52c2bda0bd42917c20a625ce995
+  data.tar.gz: 2ae4ffec963b02a83f37a3034af4af3835e9b27e018d05b7294979e716b3ec47
 SHA512:
-  metadata.gz: 2757c5a4dd8ea358a6e461239264058098c995c66dc564a123635fd3a9c79ed6dc9f32e0c1abb66f935487b19fcbb7a1c5ad80d27a1c1dff1c95e77d7ade3bca
-  data.tar.gz: a98a7299fdd7f133cdcc2b38e338768c86a01d20e2009bb1e515605d420124c41075802496efae7f995de9c23dda69fe06e409f2937e03b0fb4cdf4cd08abaa0
+  metadata.gz: 120bd8ae2bbae899b096d630b7cc050f828b0004c7cf9432cf7d4e16113d4c71d542c5ab8d32fbdb953199e5ae491aaadac0950759b371810b7c84170fc01f1f
+  data.tar.gz: 2c82352987cfcbfced6fe32bbe6a38544788b4d686277bd785a67a719ad22fef052102623388aec7bece99c059b7eb9c921bd07de695097cde7a87177f2ad26e

data/Gemfile

@@ -2,4 +2,5 @@ source 'https://rubygems.org'
 
 gem 'redis'
 gem 'sidekiq'
-gem 'workflow_manager', :path => '/srv/GT/analysis/masaomi/FGCZ/prototype_workflow_manager_with_sidekiq_20210122/workflow_manager/'
+gem 'workflow_manager', :path => './'
+#gem 'workflow_manager'

data/config/environments/redis.conf

@@ -1,6 +1,6 @@
 loglevel debug
 logfile ./logs/redis.log
-databases 4
+databases 5
 save 300 10
 rdbcompression yes
 dir ./dbs

data/lib/job_checker.rb

@@ -40,15 +40,15 @@ class JobChecker
     end
     new_job_script
   end
-  def update_time_status(status, script_basename, user, project_number)
+  def update_time_status(status, script_basename, user, project_number, next_dataset_id)
     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].join(',')
+    [status, script_basename, [@start_time, time].join("/"), user, project_number, next_dataset_id].join(',')
   end
 
-  def perform(job_id, script_basename, log_file, user, project_id)
+  def perform(job_id, script_basename, log_file, user, project_id, next_dataset_id=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 +63,10 @@ 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)
+      db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id)
 
       unless state == pre_state
-        db0[job_id] = update_time_status(state, script_basename, user, project_id)
+        db0[job_id] = update_time_status(state, script_basename, user, project_id, next_dataset_id)
         project_jobs = eval((db2[project_id]||[]).to_s)
         project_jobs = Hash[*project_jobs]
         project_jobs[job_id] = state

data/lib/workflow_manager/server.rb

@@ -163,6 +163,7 @@ module WorkflowManager
                     RedisDB.new(1, @redis_conf)
                 end
       @jobs = RedisDB.new(2, @redis_conf)
+      @trees = RedisDB.new(4, @redis_conf)
 
       @system_log = File.join(@log_dir, "system.log")
       @mutex = Mutex.new
@@ -177,6 +178,7 @@ module WorkflowManager
       log_puts("Cluster = #{@cluster.name}")
       log_puts("Server starts")
       log_puts("Recovery check")
+      sleep 2
       recovery_job_checker
     end
     def recovery_job_checker
@@ -185,12 +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 = status.split(",")
+          stat, script_basename, time, user, project_number, next_dataset_id = 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)
+            JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id)
           end
         end
       end
@@ -295,7 +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='')
+    def start_monitoring3(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='', next_dataset_id='')
       script_basename = File.basename(script_path)
       job_id, log_file, command = @cluster.submit_job(script_path, script_content, sge_options)
       #p command
@@ -303,7 +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)
+      JobChecker.perform_async(job_id, script_basename, log_file, user, project_number, next_dataset_id)
       job_id
     end
     def start_monitoring2(script_path, script_content, user='sushi_lover', project_number=0, sge_options='', log_dir='')
@@ -472,17 +474,23 @@ module WorkflowManager
       job_idsh = if job_ids
                    Hash[*(job_ids.split(',')).map{|job_id| [job_id, true]}.flatten]
                  end
-      s_ = {}
-      unless job_ids
+      if project_number
+        s_ = {}
         @jobs.transaction do |jobs|
           if project_jobs = jobs[project_number]
             s_ = Hash[*eval(project_jobs)]
           end
         end
-      end
-      @statuses.transaction do |statuses|
-        s_.each do |job_id, stat|
-          s << [job_id, statuses[job_id]]
+        @statuses.transaction do |statuses|
+          s_.each do |job_id, stat|
+            s << [job_id, statuses[job_id]]
+          end
+        end
+      else
+        @statuses.transaction do |statuses|
+          statuses.each do |key, value|
+            s << [key, value]
+          end
         end
       end
       if job_ids
@@ -548,6 +556,19 @@ module WorkflowManager
     def cluster_node_list
       @cluster.node_list
     end
+    def save_dataset_tree(project_number, json)
+      @trees.transaction do |trees|
+        trees[project_number] = json
+      end
+      json
+    end
+    def load_dataset_tree(project_number)
+      json = nil
+      @trees.transaction do |trees|
+        json = trees[project_number]
+      end
+      json
+    end
   end
 end
 

data/lib/workflow_manager/version.rb

@@ -1,3 +1,3 @@
 module WorkflowManager
-  VERSION = "0.7.2"
+  VERSION = "0.7.6"
 end

data/start_workflow_manager.sh

@@ -0,0 +1,11 @@
+#!/usr/bin/bash
+source /usr/local/ngseq/etc/lmod_profile
+module load Dev/Ruby/2.6.7
+module load Tools/Redis/6.0.1
+conda activate gtools_env
+which python
+which g-sub
+which g-req
+mkdir -p logs
+mkdir -p dbs
+bundle exec workflow_manager -d druby://fgcz-h-031:40001

data/test/job_list.rb

@@ -1,13 +1,13 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20210723-134812'
+# Version = '20211001-104513'
 
 PORT = (ARGV[0]||6380).to_i
 require 'redis'
 db0 = Redis.new(port: PORT, db: 0)
 db1 = Redis.new(port: PORT, db: 1)
 db2 = Redis.new(port: PORT, db: 2)
-#db3 = Redis.new(port: 6380, db: 3)
+db4 = Redis.new(port: PORT, db: 4)
 
 class Redis
   def show_all
@@ -18,8 +18,8 @@ class Redis
   end
 end
 
-dbs = [db0, db1, db2]
-db_notes = ["state DB", "log DB", "project job DB"]
+dbs = [db0, db1, db2, db4]
+db_notes = ["state DB", "log DB", "project job DB", "JS tree DB"]
 
 dbs.each.with_index do |db, i|
   note = db_notes[i]
@@ -48,3 +48,10 @@ db2.keys.sort.each do |key|
   value = db2.get(key)
   puts [key, value].join("\t")
 end
+
+puts
+puts "db3, status DB3, project specific"
+db3.keys.sort.each do |key|
+  value = db3.get(key)
+  puts [key, value].join("\t")
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: workflow_manager
 version: !ruby/object:Gem::Version
-  version: 0.7.2
+  version: 0.7.6
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-07-30 00:00:00.000000000 Z
+date: 2021-10-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -87,6 +87,7 @@ files:
 - spec/cluster_spec.rb
 - spec/server_spec.rb
 - spec/spec_helper.rb
+- start_workflow_manager.sh
 - test/call_worker4.rb
 - test/call_worker_method.rb
 - test/job_list.rb