scout-gear 1.1.1 → 2.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5d3dbd13f983d86074eefff6b693c2d0ae45ae9f7c575201df0a43e6f67fdf21
-  data.tar.gz: 1a9c3aec79e50876d43953bac3a3b8b1b35ba158edf649466e6ceba9c7a8b5da
+  metadata.gz: 7af276a76f116d6ba9dc7a995c55dbefd5d432a5df4d0b13b7335e1f8581a48c
+  data.tar.gz: 2aae18d093c071a844ec2780fa79b5caabc0127c88938873d5e07e8eeeb21ce8
 SHA512:
-  metadata.gz: 32672c88eb7fe8627b8d499d136cf5023fd3709e172731cbdb1b4fd2ca22fcdee45f36f0cf6522ab6907e085815458b422487a4afe9db22af43c6ba65e587227
-  data.tar.gz: '09452083132409f72b7509dad2db27d834b183017900223c9678ef900e1e69259f5af444454f38084cb848c21364d717a2364bdc90e380c4972e1029d306133c'
+  metadata.gz: 5d642aab0bcb89f0e0c06de0ae0fadb0295170c66faee5188bd2eb23ee4366e776ec9c3ddb675b4ab15394e45c493896a917d6e29f04bc024b08ed7829cf6263
+  data.tar.gz: b2f370a8088d8abb4b4e7955da2c8616cf5af4b6bca88e8578442505ef1cfb9477927e5ccb6522208bdf1520a9b3fec46e53bbacfbee636a218fa1e33fd05330

data/.gitmodules

@@ -0,0 +1,4 @@
+[submodule "modules/rbbt-util"]
+	path = modules/rbbt-util
+	url = https://github.com/mikisvaz/rbbt-util.git
+	branch = scout

data/.vimproject

@@ -1,12 +1,18 @@
 scout-gear=/$PWD filter="*.rb *.yaml" {
  Rakefile
  bin=bin {
+  scout
  }
  lib=lib {
   scout-gear.rb
   scout=scout{
-   exceptions.rb
    meta_extension.rb
+   exceptions.rb
+
+   misc.rb
+   misc=misc{
+    format.rb
+   }
    tmpfile.rb
    indiferent_hash.rb
    indiferent_hash=indiferent_hash{
@@ -24,9 +30,18 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
      util.rb
     }
    }
+   simple_opt.rb
+   simple_opt=simple_opt{
+    accessor.rb
+    doc.rb
+    parse.rb
+    get.rb
+    setup.rb
+   }
    path.rb
    path=path{
     find.rb
+    util.rb
    }
   }
  }
@@ -41,5 +56,593 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
    test_tmpfile.rb
   }
  }
+
+ modules=modules{
+  rbbt-util=rbbt-util filter="*.rb *.rake Rakefile *.rdoc *.R *.sh *.js *.haml *.sass *.txt *.conf LICENSE" {
+   Migration-1.9.txt
+   Troubleshooting.txt
+   ToDo.txt
+   Rakefile
+   LICENSE
+   README.rdoc
+   bin=bin filter="*" {
+    excel2tsv.rb
+    rbbt
+    rbbt_Rutil.rb
+    rbbt_dangling_locks.rb
+    rbbt_exec.rb
+    rbbt_query.rb
+    rbbt_find.rb
+   }
+   lib=lib{
+    rbbt.rb
+
+    rbbt-util.rb
+
+    rbbt=rbbt{
+     refactor.rb
+
+     util=util{
+      misc.rb
+      misc=misc{
+       serialize.rb
+       exceptions.rb
+       concurrent_stream.rb
+       indiferent_hash.rb
+       pipes.rb
+       format.rb
+       omics.rb
+       inspect.rb
+       math.rb
+       development.rb
+       lock.rb
+       options.rb
+       system.rb
+       objects.rb
+       manipulation.rb
+       bgzf.rb
+       multipart_payload.rb
+       annotated_module.rb
+       communication.rb
+      }
+      version.rb
+      tar.rb
+      color.rb
+      colorize.rb
+      named_array.rb
+      cmd.rb
+      docker.rb
+      config.rb
+      log.rb
+      log=log{
+       refactor.rb
+       progress.rb
+       progress=progress{
+        util.rb
+        report.rb
+       }
+      }
+      open.rb
+      semaphore.rb
+
+      simpleopt.rb
+      simpleopt=simpleopt{
+       accessor.rb
+       doc.rb
+       parse.rb
+       get.rb
+       setup.rb
+      }
+
+      ssh.rb
+
+      simpleDSL.rb
+
+      chain_methods.rb
+
+      tmpfile.rb
+      tc_cache.rb
+      filecache.rb
+
+      R.rb
+      R=R{
+       eval.rb
+       model.rb
+       plot.rb
+      }
+
+      python.rb
+      python=python{
+       util.rb
+      }
+
+      excel2tsv.rb
+
+      concurrency.rb
+      concurrency=concurrency{
+       processes.rb
+       threads.rb
+     processes=processes{
+      socket.rb
+      worker.rb
+     }
+    }
+
+    procpath.rb
+
+    migrate.rb
+   }
+
+   monitor.rb
+
+   workflow.rb
+   workflow=workflow{
+    annotate.rb
+
+    definition.rb
+    dependencies.rb
+
+    accessor.rb
+
+    task.rb
+
+    step.rb
+    step=step{
+     accessor.rb
+     dependencies.rb
+     info.rb
+     prepare.rb
+     run.rb
+     save_load_inputs.rb
+     status.rb
+    }
+
+    examples.rb
+    doc.rb
+    usage.rb
+
+    soap.rb
+
+    util=util{
+     archive.rb
+     provenance.rb
+     orchestrator.rb
+     trace.rb
+     data.rb
+    }
+
+    remote_workflow.rb
+    remote_workflow=remote_workflow{
+     driver.rb
+     driver=driver{
+      rest.rb
+      ssh.rb
+     }
+
+     remote_step.rb
+     remote_step=remote_step{
+      rest.rb
+      ssh.rb
+     }
+    }
+
+    integration=integration{
+     cromwell.rb
+     nextflow.rb
+     ansible.rb
+     ansible=ansible{
+      workflow.rb
+     }
+    }
+   }
+
+   hpc.rb
+   hpc=hpc{
+    old=old{
+     slurm.rb
+    }
+    orchestrate.old.rb
+
+    batch.rb
+    slurm.rb
+    lsf.rb
+
+    orchestrate.rb
+    orchestrate=orchestrate{
+     rules.rb
+     chains.rb
+     batches.rb
+    }
+    trace.rb
+   }
+
+   tsv.rb
+   tsv=tsv{
+    parser.rb
+    dumper.rb
+
+    matrix.rb
+
+    accessor.rb
+    util.rb
+    marshal.rb
+    serializers.rb
+    manipulate.rb
+    index.rb
+    stream.rb
+    attach.rb
+    attach=attach{
+     util.rb
+    }
+    melt.rb
+    excel.rb
+    csv.rb
+    filter.rb
+    field_index.rb
+    change_id.rb
+    parallel.rb
+    parallel=parallel{
+     traverse.rb
+     through.rb
+    }
+   }
+
+   packed_index.rb
+   fix_width_table.rb
+
+   persist.rb
+   persist=persist{
+    tsv.rb
+    tsv=tsv{
+     adapter.rb
+
+     sharder.rb
+     tokyocabinet.rb
+     tokyocabinet=tokyocabinet{
+      marshal.rb
+     }
+     fix_width_table.rb
+     packed_index.rb
+     kyotocabinet.rb
+     lmdb.rb
+     cdb.rb
+     leveldb.rb
+    }
+   }
+
+   resource.rb
+   resource=resource{
+    path.rb
+    util.rb
+    with_key.rb
+    rake.rb
+   }
+
+   annotations.rb
+   annotations=annotations{
+    util.rb
+    annotated_array.rb
+   }
+
+   entity.rb
+   entity=entity{
+    identifiers.rb
+   }
+
+   association.rb
+   association=association{
+    util.rb
+    database.rb
+    open.rb
+    index.rb
+    item.rb
+   }
+
+   knowledge_base.rb
+   knowledge_base=knowledge_base{
+    enrichment.rb
+    entity.rb
+    query.rb
+    registry.rb
+    syndicate.rb
+    traverse.rb
+   }
+  }
+ }
+ test=test {
+  test_helper.rb
+  data=data filter="*"{
+   Test.xls
+   dose_response
+   dose_response2
+   dose_response3
+   example.pdf
+   gene_ages
+   identifiers
+   test.tsv
+  }
+  rbbt=rbbt{
+   test_annotations.rb
+   test_association.rb
+   test_entity.rb
+   test_fix_width_table.rb
+   test_knowledge_base.rb
+   test_monitor.rb
+   test_packed_index.rb
+   test_persist.rb
+   test_resource.rb
+   test_tsv.rb
+   test_workflow.rb
+   resource=resource{
+    test_path.rb
+    }
+   workflow=workflow{
+    _test_soap.rb
+    test_doc.rb
+    test_step.rb
+    test_task.rb
+   }
+   association=association{
+    test_database.rb
+    test_index.rb
+    test_item.rb
+    test_open.rb
+    test_util.rb
+   }
+   knowledge_base=knowledge_base{
+    test_enrichment.rb
+    test_query.rb
+    test_registry.rb
+    }
+   persist=persist{
+    tsv=tsv{
+     test_cdb.rb
+     test_kyotocabinet.rb
+     test_leveldb.rb
+     test_lmdb.rb
+     test_sharder.rb
+     test_tokyocabinet.rb
+     }
+    test_tsv.rb
+   }
+   tsv=tsv{
+    test_accessor.rb
+    test_attach.rb
+    test_change_id.rb
+    test_csv.rb
+    test_excel.rb
+    test_field_index.rb
+    test_filter.rb
+    test_index.rb
+    test_manipulate.rb
+    test_matrix.rb
+    test_parallel.rb
+    test_parser.rb
+    test_stream.rb
+    test_util.rb
+    parallel=parallel{
+     test_through.rb
+     test_traverse.rb
+    }
+   }
+   entity=entity{
+    test_identifiers.rb
+   }
+   util=util{
+    test_R.rb
+    test_chain_methods.rb
+    test_cmd.rb
+    test_colorize.rb
+    test_concurrency.rb
+    test_config.rb
+    test_excel2tsv.rb
+    test_filecache.rb
+    test_log.rb
+    test_misc.rb
+    test_open.rb
+    test_python.rb
+    test_semaphore.rb
+    test_simpleDSL.rb
+    test_simpleopt.rb
+    test_tmpfile.rb
+    R=R{
+     test_eval.rb
+     test_model.rb
+     test_plot.rb
+    }
+    misc=misc{
+     test_bgzf.rb
+     test_format.rb
+     test_lock.rb
+     test_multipart_payload.rb
+     test_omics.rb
+     test_pipes.rb
+    }
+    simpleopt=simpleopt{
+     test_get.rb
+     test_parse.rb
+     test_setup.rb
+    }
+    concurrency=concurrency{
+     test_processes.rb
+     test_threads.rb
+     }
+   }
+  }
+ }
+ python=python filter="*"{
+  rbbt.py
+ }
+ integration_test=integration_test{
+  test_bed.rb
+  test_helper.rb
+  test_namespaces.rb
+  test_workflow.rb
+ }
+ etc=etc filter="*"{
+  app.d=app.d{
+   init.rb
+
+   base.rb
+
+   requires.rb
+   entities.rb
+   finder.rb
+   foundation.rb
+   grid_system.rb
+   knowledge_bases.rb
+   resources.rb
+   workflows.rb
+   semaphores.rb
+   remote_workflow_tasks.rb
+  }
+ }
+ share=share{
+  config.ru
+  workflow_config.ru
+  unicorn.rb
+  color=color filter="*"{
+   diverging_colors.hex
+   color_names
+  }
+  rbbt_commands=rbbt_commands filter="*"{
+   alias
+   ansible
+   check_bgzf
+   cmd
+   color
+   log
+   migrate
+   migrate_job
+   purge_job
+   rsync
+   watch
+   system=system{
+    clean
+    deleted_files
+    optimize
+    purge
+    report
+    status
+   }
+   conf=conf{
+    web_user=web_user{
+     add
+     list
+     remove
+    }
+   }
+   resource=resource{
+    exists
+    find
+    glob
+    get
+    produce
+    read
+   }
+   workflow=workflow{
+    archive
+    archive_all
+    cmd
+    example
+    forget_deps
+    info
+    write_info
+    init
+    install
+    jobs
+    knowledge_base
+    list
+    monitor
+    prov
+    server
+    task
+    trace
+    remote=remote{
+     add
+     list
+     remove
+    }
+   }
+   hpc=hpc{
+    task
+    orchestrate
+    tail
+    list
+    clean
+   }
+   app=app{
+    install
+    start
+    template
+   }
+   association=association{
+    subset
+   }
+   tsv=tsv{
+    assemble_pdf_table
+    attach
+    change_id
+    collapse
+    get
+    head
+    info
+    json
+    keys
+    query
+    read
+    read_excel
+    slice
+    sort
+    subset
+    select
+    transpose
+    uncollapse
+    unzip
+    values
+    write_excel
+    zip
+    view
+   }
+   stat=stat{
+    abs
+    boxplot
+    compare_lists
+    density
+    heatmap
+    log
+    pvalue.qqplot
+   }
+   study=study{
+    maf2study
+    task
+   }
+   file_server=file_server{
+    add
+    list
+    remove
+   }
+   benchmark=benchmark{
+    pthrough
+    throughput
+    tsv
+   }
+  }
+  Rlib=Rlib{
+   plot.R
+   svg.R
+   util.R
+  }
+  software=install/software filter="*"{
+   zran=zran{
+    zran.c
+   }
+   lib=lib{
+    install_helpers
+   }
+  }
+ }
 }
 
+ }
+}

data/Rakefile

@@ -50,4 +50,5 @@ Rake::RDocTask.new do |rdoc|
   rdoc.title = "scout-gear #{version}"
   rdoc.rdoc_files.include('README*')
   rdoc.rdoc_files.include('lib/**/*.rb')
+  rdoc.rdoc_files.include('../modules/rbbt-util/lib/**/*.rb')
 end

data/VERSION

@@ -1 +1 @@
-1.1.1
+2.0.0

data/bin/scout

@@ -0,0 +1,28 @@
+#!/usr/bin/env ruby
+
+require_relative '../lib/scout-gear'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+
+case
+when File.exist?(file = File.join(__dir__, '../modules/rbbt-util/bin/rbbt'))
+  $LOAD_PATH.unshift(lib_dir = File.join(file, '../..', 'lib'))
+  require_relative File.join(lib_dir,'rbbt-util')
+  Path.add_path(:rbbt, File.expand_path(File.join(File.dirname(lib_dir), "/{TOPLEVEL}/{SUBPATH}")))
+  Path.default_pkgdir = Rbbt
+  load file
+when File.exist?(file = File.join(ENV["HOME"], 'git/scout-gear/modules/rbbt-util/bin/rbbt'))
+  $LOAD_PATH.unshift(lib_dir = File.join(file, '../..', 'lib'))
+  require_relative File.join(lib_dir,'rbbt-util')
+  Path.add_path(:rbbt, File.expand_path(File.join(File.dirname(lib_dir), "/{TOPLEVEL}/{SUBPATH}")))
+  Path.default_pkgdir = Rbbt
+  load file
+when File.exist?(file = File.join(ENV["HOME"], 'git/rbbt-util/bin/rbbt'))
+  $LOAD_PATH.unshift(lib_dir = File.join(file, '../..', 'lib'))
+  require_relative File.join(lib_dir,'rbbt-util')
+  Path.add_path(:rbbt, File.expand_path(File.join(File.dirname(lib_dir), "/{TOPLEVEL}/{SUBPATH}")))
+  Path.default_pkgdir = Rbbt
+  load file
+else
+  raise "Cant find rbbt"
+end

data/lib/scout/indiferent_hash.rb

@@ -75,33 +75,3 @@ module IndiferentHash
   end
 end
 
-module CaseInsensitiveHash
-
-  def self.setup(hash)
-    hash.extend CaseInsensitiveHash
-  end
-
-  def downcase_keys
-    @downcase_keys ||= begin
-                         down = {} 
-                         keys.collect{|key| 
-                           down[key.to_s.downcase] = key 
-                         }
-                         down
-                       end
-  end
-
-  def [](key, *rest)
-    value = super(key, *rest)
-    return value unless value.nil?
-    key_downcase = key.to_s.downcase
-    super(downcase_keys[key_downcase])
-  end
-
-  def values_at(*keys)
-    keys.collect do |key|
-      self[key]
-    end
-  end
-  
-end

data/lib/scout/log/progress/report.rb

@@ -208,7 +208,7 @@ module Log
       done_msg << Log.color(:magenta, " · " << desc)
       print(io, Log.up_lines(@depth) << done_msg << Log.down_lines(@depth)) 
 
-      FileUtils.rm file if file and File.exists?(file)
+      FileUtils.rm file if file and File.exist?(file)
 
       @callback.call self if @callback
     end