rbbt-util 5.26.151 → 5.26.152

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA256:
-  metadata.gz: 11b833bbcd15bc363a8bc7923828bc7545c276f79d9ed2d41a1078e8d57fff10
-  data.tar.gz: 83bfc6713a4333ae904cd8636eb8e9724545085d1c4aff1973b534287521d342
+SHA1:
+  metadata.gz: 85aa7a358c16c13eeb0528c2f67a8eacc94d6aef
+  data.tar.gz: b4d62fb09f600f50c973dc0eb53a195a7fb9752a
 SHA512:
-  metadata.gz: 23f47354eba951a3d299b132c25e096d6de81e3e1254fda1a5a6b0a245455139c9bfcbf4db4d20ca50b7d91828a04fdca517109235ffd4fae69feb118f252392
-  data.tar.gz: a3fbc000a6626b94da9a6895a473a1300b388e7350d05327cd824e3a027a7ca50c5c761a29fe7c52b39ea66be8e89f81c6c76137ee6283be0a1ad254e95b4960
+  metadata.gz: d07f838e26b9c02495367a6d886eae1b092c230b1c6b622267e04d972e4216ebbef4c04bc489595a5dca429147ad0ed9b6fd5c901e65eb13036d94aa10521d3c
+  data.tar.gz: f95e14b56df996c1a57e269807bdf578eae7dcb5216debc7630d01d5e18fde66a35a573cf7f52d45239de825451da65b5a800156c0c5922a6e0c843ef2e01e32

data/lib/rbbt/util/version.rb

@@ -3,6 +3,7 @@ module Rbbt
 
   def self.add_version(file)
     dir = Path.setup(Path.caller_lib_dir(file))
+    return if dir.nil?
     libname = File.basename(dir).sub('rbbt-','')
     return if VERSIONS.include? libname
 

data/lib/rbbt/workflow/doc.rb

@@ -35,6 +35,7 @@ module Workflow
   end
 
   def documentation_markdown
+    return "" if @libdir.nil?
     file = @libdir['workflow.md'].find
     if file.exists?
       file.read

data/lib/rbbt/workflow/remote/rest/adaptor.rb

@@ -78,10 +78,10 @@ module WorkflowRESTClient
 
   def init_remote_tasks
     task_exports = WorkflowRESTClient.get_json(url)
-    @asynchronous_exports = task_exports["asynchronous"].collect{|task| task.to_sym }
-    @synchronous_exports = task_exports["synchronous"].collect{|task| task.to_sym }
-    @exec_exports = task_exports["exec"].collect{|task| task.to_sym }
-    @stream_exports = task_exports["stream"].collect{|task| task.to_sym }
+    @asynchronous_exports = (task_exports["asynchronous"] || []).collect{|task| task.to_sym }
+    @synchronous_exports = (task_exports["synchronous"] || []).collect{|task| task.to_sym }
+    @exec_exports = (task_exports["exec"] || []).collect{|task| task.to_sym }
+    @stream_exports = (task_exports["stream"] || []).collect{|task| task.to_sym }
     @can_stream = task_exports["can_stream"]
   end
 

data/lib/rbbt/workflow.rb

@@ -36,7 +36,9 @@ module Workflow
 
   def self.extended(base)
     self.workflows << base
-    base.libdir = Path.setup(Path.caller_lib_dir).tap{|p| p.resource = base}
+    libdir = Path.caller_lib_dir
+    return if libdir.nil?
+    base.libdir = Path.setup(libdir).tap{|p| p.resource = base}
   end
 
   def self.init_remote_tasks

data/share/rbbt_commands/app/start

@@ -85,7 +85,7 @@ Misc.in_dir(app_dir) do
 
   case server
   when 'passenger'
-    system ENV, "env RBBT_LOG=0 passenger start -R '#{config_ru_file}' -p #{options[:port] || "2887"}"
+    system ENV, "env RBBT_LOG=0 passenger start -R '#{config_ru_file}' -p #{options[:Port] || "2887"}"
   when 'puma_alt'
     system ENV, "puma '#{config_ru_file}' -p #{options[:Port] || "2887"} -w 3 -t 8:32 --preload"
   else

data/share/rbbt_commands/workflow/server

@@ -111,7 +111,7 @@ TmpFile.with_file do |app_dir|
 
     case server
     when 'unicorn'
-      `env RBBT_LOG=#{Log.severity.to_s} unicorn -c #{ Rbbt.share['unicorn.rb'].find } '#{config_ru_file}' -p #{options[:port] || "2887"}`
+      `env RBBT_LOG=#{Log.severity.to_s} unicorn -c #{ Rbbt.share['unicorn.rb'].find } '#{config_ru_file}' -p #{options[:Port] || "2887"}`
     when 'puma_alt'
       #`puma '#{config_ru_file}' -p #{options[:Port] || "2887"} -w 3 -t 8:32 --preload`
       `env RBBT_LOG=#{Log.severity.to_s} puma '#{config_ru_file}' -p #{options[:Port] || "2887"} -w 20 -t 10:160 --preload`

data/share/rbbt_commands/workflow/trace

@@ -18,11 +18,12 @@ $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_c
 options = SOPT.setup <<EOF
 Examine the provenance of a job result
 
-$ rbbt workflow trace <job-result> <file.png>
+$ rbbt workflow trace <job-result>
 
 -h--help Help
 -w--width* Image Width
 -h--height* Image Height
+-p--plot Plot file
 -s--size* Image Size (Height and Width)
 -fg--fix_gap Remove execution gaps
 -pd--plot_data Print plot data
@@ -30,8 +31,8 @@ EOF
 
 SOPT.usage if options[:help]
 
-file = ARGV.shift || "/home/mvazque2/.rbbt/var/jobs/Sample/haplotype/NA12878"
-plot = ARGV.shift 
+files = ARGV
+plot = options[:plot]
 
 width, height, size = options.values_at :width, :height, :size
 
@@ -45,20 +46,22 @@ def get_step(file)
   Workflow.load_step file
 end
 
-step = get_step file
+jobs = []
+files.each do |file|
+  step = get_step file
 
+  jobs += step.rec_dependencies + [step]
 
-jobs = step.rec_dependencies + [step]
-
-step.info[:archived_info].each do |path,ainfo|
-  archived_step = Step.new path
-  class << archived_step
-    self
-  end.define_method :info do
-    ainfo
-  end
-  jobs << archived_step
-end if step.info[:archived_info]
+  step.info[:archived_info].each do |path,ainfo|
+    archived_step = Step.new path
+    class << archived_step
+      self
+    end.define_method :info do
+      ainfo
+    end
+    jobs << archived_step
+  end if step.info[:archived_info]
+end
 
 jobs = jobs.select{|job| job.info[:done]}.sort_by{|job| job.info[:started]}
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.151
+  version: 5.26.152
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-03-18 00:00:00.000000000 Z
+date: 2020-03-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -537,93 +537,94 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.6
+rubyforge_project: 
+rubygems_version: 2.5.2.3
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_entity.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/remote/test_client.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_lock.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/test_association.rb
 - test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/misc/test_omics.rb
 - test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/misc/test_lock.rb
+- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/test_config.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/R/test_eval.rb
 - test/rbbt/util/R/test_model.rb
-- test/rbbt/util/test_config.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/test_cmd.rb
 - test/rbbt/util/test_log.rb
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/log/test_progress.rb
 - test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
 - test/rbbt/util/test_python.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_chain_methods.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_fix_width_table.rb
 - test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_stream.rb
 - test/rbbt/tsv/test_excel.rb
 - test/rbbt/tsv/parallel/test_through.rb
 - test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/test_association.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_fix_width_table.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_parallel.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_parser.rb
 - test/rbbt/test_workflow.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_hpc.rb
-- test/rbbt/test_monitor.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/test_annotations.rb
 - test/rbbt/test_persist.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/remote/test_client.rb
 - test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
 - test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_query.rb
 - test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_hpc.rb
+- test/rbbt/resource/test_path.rb
+- test/rbbt/test_entity.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/test_tsv.rb
 - test/test_helper.rb